diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index b98cbb99092..2bcd47ee161 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 3edf7c221aa..d8c7405c6e4 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -4,8 +4,8 @@ process CUSTOM_GETCHROMSIZES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap index c37b284d761..d2072e22c62 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap @@ -27,7 +27,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -54,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:38:36.927106" + "timestamp": "2024-10-18T10:11:37.459094476" }, "test_custom_getchromsizes": { "content": [ @@ -87,7 +87,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -109,15 +109,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:22:34.14237" + "timestamp": "2024-10-18T10:11:01.526301351" }, "test_custom_getchromsizes_bgzip": { "content": [ @@ -147,7 +147,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -174,15 +174,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:23:06.241379" + "timestamp": "2024-10-18T10:11:14.32456385" }, "test_custom_getchromsizes - stub": { "content": [ @@ -207,7 +207,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -229,14 +229,14 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:24:05.697845" + "timestamp": "2024-10-18T10:11:26.505487624" } } \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index 9f5f9fb9b47..9824d0c277a 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - python=3.9.5 + - python=3.10.4 diff --git a/modules/nf-core/custom/tx2gene/main.nf b/modules/nf-core/custom/tx2gene/main.nf index 99c00aa0692..eed5e97b1cc 100644 --- a/modules/nf-core/custom/tx2gene/main.nf +++ b/modules/nf-core/custom/tx2gene/main.nf @@ -4,8 +4,8 @@ process CUSTOM_TX2GENE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'biocontainers/python:3.9--1' }" + 'https://depot.galaxyproject.org/singularity/python:3.10.4' : + 'biocontainers/python:3.10.4' }" input: tuple val(meta), path(gtf) diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index c19f10f7162..2be5fe547d1 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ], "tx2gene": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:13:11.305047" + "timestamp": "2024-10-18T10:24:12.19104487" }, "saccharomyces_cerevisiae - gtf - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ], "tx2gene": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T15:15:34.064489" + "timestamp": "2024-10-18T10:24:24.729694098" } } \ No newline at end of file diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 3f03c6808a5..5a71e085afe 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process PICARD_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index f823197d284..3ae6b917141 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.replaced.cram", [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:54:40.471730168" + "timestamp": "2024-10-18T10:13:23.115450366" }, "sarscov2 - bam - stub": { "content": [ @@ -30,7 +30,7 @@ ], "3": [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ], "bai": [ @@ -47,28 +47,28 @@ ], "versions": [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:55:08.402649243" + "timestamp": "2024-10-18T10:13:47.23694937" }, "sarscov2 - bam": { "content": [ "null.replaced.bam", "null.replaced.bai", [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:54:22.239968953" + "timestamp": "2024-10-18T10:12:53.083677142" } } \ No newline at end of file diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/bedtointervallist/environment.yml +++ b/modules/nf-core/picard/bedtointervallist/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf index 2cc6cbd2f0f..c8eddb1a12e 100644 --- a/modules/nf-core/picard/bedtointervallist/main.nf +++ b/modules/nf-core/picard/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process PICARD_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta) , path(bed) diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap index 6abbf0e92f9..7382eafc851 100644 --- a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap +++ b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65" + "versions.yml:md5,33540ea0c31ded2c1db95f82406034f8" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65" + "versions.yml:md5,33540ea0c31ded2c1db95f82406034f8" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:39:08.82372" + "timestamp": "2024-10-18T10:17:35.308452582" } } \ No newline at end of file diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/cleansam/environment.yml +++ b/modules/nf-core/picard/cleansam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 7b95cebdc0f..f2ab79bd53b 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -4,8 +4,8 @@ process PICARD_CLEANSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap index 63e2927e57a..efecdb5efe3 100644 --- a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap +++ b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "798439cbd7fd81cbcc5078022dc5479d", [ - "versions.yml:md5,f99b648dc3d150a0561094e3a142ee22" + "versions.yml:md5,412651954aecab12c868ee78cf9fa724" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:36:05.525364" + "timestamp": "2024-10-18T10:46:32.969920917" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/picard/collecthsmetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index a9cbafd44f2..1d017ef8db2 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTHSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap index 53855d13b68..4d21710a062 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap @@ -106,26 +106,26 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:45:46.991614248" + "timestamp": "2024-10-18T10:51:55.291163084" }, "versions": { "content": [ [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:36:50.350567213" + "timestamp": "2024-10-18T10:51:30.748857589" }, "sarscov2 - bam - samebed": { "content": [ @@ -234,14 +234,14 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:46:33.770516478" + "timestamp": "2024-10-18T10:52:43.803456585" }, "sarscov2 - bam": { "content": [ @@ -350,14 +350,14 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:45:16.117386245" + "timestamp": "2024-10-18T10:51:01.881343611" }, "sarscov2 - bam - bed": { "content": [ @@ -466,13 +466,13 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:46:13.489487836" + "timestamp": "2024-10-18T10:52:22.830749735" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf index 1a49a7f0af2..c3014d806c9 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf +++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTINSERTSIZEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap index bcb5b4557b7..cbe9329d052 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap @@ -9,14 +9,14 @@ ], "test.pdf", [ - "versions.yml:md5,4423bfe2194f61d919c382d2225b0835" + "versions.yml:md5,38d39e9882afe7ac015213c286745056" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T12:23:29.392944" + "timestamp": "2024-10-18T10:55:45.769771444" }, "test-picard-collectinsertsizemetrics-stub": { "content": [ @@ -40,7 +40,7 @@ ] ], "2": [ - "versions.yml:md5,4423bfe2194f61d919c382d2225b0835" + "versions.yml:md5,38d39e9882afe7ac015213c286745056" ], "histogram": [ [ @@ -61,14 +61,14 @@ ] ], "versions": [ - "versions.yml:md5,4423bfe2194f61d919c382d2225b0835" + "versions.yml:md5,38d39e9882afe7ac015213c286745056" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T12:20:03.841884" + "timestamp": "2024-10-18T10:56:09.914953495" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index c5555871dc3..cf1af40af3c 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta) , path(bam), path(bai) diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap index 1859541b6dd..a76a3237577 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap @@ -16,14 +16,14 @@ "test.CollectMultipleMetrics.read_length_histogram.pdf" ], [ - "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:03:36.631174" + "timestamp": "2024-10-18T11:05:12.591021247" }, "test-picard-collectmultiplemetrics-cram": { "content": [ @@ -42,14 +42,14 @@ "test.CollectMultipleMetrics.read_length_histogram.pdf" ], [ - "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:04:13.955902" + "timestamp": "2024-10-18T11:06:08.499320579" }, "test-picard-collectmultiplemetrics-nofasta": { "content": [ @@ -68,13 +68,13 @@ "test.CollectMultipleMetrics.read_length_histogram.pdf" ], [ - "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:03:54.707587" + "timestamp": "2024-10-18T11:05:42.117033611" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf index 0c8f2cfa2c1..eb80fdc70c2 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/main.nf +++ b/modules/nf-core/picard/collectrnaseqmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTRNASEQMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test new file mode 100644 index 00000000000..9ab1855217a --- /dev/null +++ b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test @@ -0,0 +1,81 @@ +nextflow_process { + + name "Test Process PICARD_COLLECTRNASEQMETRICS" + script "../main.nf" + process "PICARD_COLLECTRNASEQMETRICS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/collectrnaseqmetrics" + tag "ucsc/gtftogenepred" + + setup { + run("UCSC_GTFTOGENEPRED") { + script "../../../ucsc/gtftogenepred/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + test("sarscov2 - fasta - gtf") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = UCSC_GTFTOGENEPRED.out.refflat.map{ it[1] } + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.metrics[0][1]).text.contains('CollectRnaSeqMetrics') }, + { assert snapshot( + process.out.versions, + process.out.pdf + ).match() } + ) + } + } + + test("sarscov2 - fasta - gtf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = UCSC_GTFTOGENEPRED.out.refflat.map{ it[1] } + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap new file mode 100644 index 00000000000..ad6503afdfb --- /dev/null +++ b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "sarscov2 - fasta - gtf": { + "content": [ + [ + "versions.yml:md5,8d0867f89947c081711de09338138c2e" + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:10:39.199344417" + }, + "sarscov2 - fasta - gtf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.rna_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,8d0867f89947c081711de09338138c2e" + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.rna_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pdf": [ + + ], + "versions": [ + "versions.yml:md5,8d0867f89947c081711de09338138c2e" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:10:57.248132065" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config b/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config similarity index 81% rename from tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config rename to modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config index 9bdb2070dbc..bc82e10c1b5 100644 --- a/tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config +++ b/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config @@ -1,11 +1,7 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName:UCSC_GTFTOGENEPRED { ext.args = "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" } - withName:PICARD_COLLECTRNASEQMETRICS { ext.args = { ( meta.strandedness == "forward" || meta.single_end ) ? "--STRAND_SPECIFICITY FIRST_READ_TRANSCRIPTION_STRAND" : @@ -13,7 +9,5 @@ process { "--STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND" : "--STRAND_SPECIFICITY NONE" } - } - } diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml index 58d52581862..13265842fcf 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 - - r::r-base + - bioconda::picard=3.3.0 + - conda-forge::r-base=4.4.1 diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 6002a7ca95c..39cf7d2b7d1 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTWGSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap index f188382b038..1958fcdebe2 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap @@ -3,26 +3,26 @@ "content": [ true, [ - "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe" + "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T11:02:46.301176" + "timestamp": "2024-10-18T10:15:18.13771243" }, "test-picard-collectwgsmetrics": { "content": [ true, [ - "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe" + "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T11:02:25.132069" + "timestamp": "2024-10-18T10:14:57.786056996" } } \ No newline at end of file diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/createsequencedictionary/environment.yml +++ b/modules/nf-core/picard/createsequencedictionary/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 4630a0d51e2..49637d1840c 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process PICARD_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap index 3f3f8c8ec90..8142f2af32f 100644 --- a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999" + "versions.yml:md5,3ed186b70c3df55fd4965f48485a01cb" ], "reference_dict": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999" + "versions.yml:md5,3ed186b70c3df55fd4965f48485a01cb" ] } ], @@ -30,19 +30,19 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-19T07:02:59.686224426" + "timestamp": "2024-10-18T10:49:55.602683425" }, "sarscov2 - fasta": { "content": [ "test.dict", [ - "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999" + "versions.yml:md5,3ed186b70c3df55fd4965f48485a01cb" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-16T14:31:34.330709472" + "timestamp": "2024-10-18T10:49:40.396060224" } } \ No newline at end of file diff --git a/modules/nf-core/picard/crosscheckfingerprints/environment.yml b/modules/nf-core/picard/crosscheckfingerprints/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/environment.yml +++ b/modules/nf-core/picard/crosscheckfingerprints/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index f6df55ade7b..61afa661505 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -4,8 +4,8 @@ process PICARD_CROSSCHECKFINGERPRINTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(input1), path(input1_index), path(input2), path(input2_index), path(haplotype_map) diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap index f283f13305f..f9e6963a445 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap +++ b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap @@ -22,25 +22,25 @@ "Crosscheck versions stub": { "content": [ [ - "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89" + "versions.yml:md5,baa5c1b1dc10b95cb42ea1b3d66a294f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:57:33.939689662" + "timestamp": "2024-10-18T11:02:39.2311109" }, "Crosscheck versions - bam": { "content": [ [ - "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89" + "versions.yml:md5,baa5c1b1dc10b95cb42ea1b3d66a294f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:57:08.745266455" + "timestamp": "2024-10-18T11:02:13.953034883" } } \ No newline at end of file diff --git a/modules/nf-core/picard/extractfingerprint/environment.yml b/modules/nf-core/picard/extractfingerprint/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/extractfingerprint/environment.yml +++ b/modules/nf-core/picard/extractfingerprint/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/extractfingerprint/main.nf b/modules/nf-core/picard/extractfingerprint/main.nf index 68b53233045..79b71f58ebb 100644 --- a/modules/nf-core/picard/extractfingerprint/main.nf +++ b/modules/nf-core/picard/extractfingerprint/main.nf @@ -4,8 +4,8 @@ process PICARD_EXTRACTFINGERPRINT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap index a754ef93e28..4b71c2f07bc 100644 --- a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap +++ b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,cbf898a998bb9b90d2e4110ee343d674" + "versions.yml:md5,5dd134f2a6a47c9592e2d77e007194db" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:53:08.359314244" + "timestamp": "2024-10-18T11:01:27.275230101" }, "extract_fingerprint": { "content": [ diff --git a/modules/nf-core/picard/fastqtosam/environment.yml b/modules/nf-core/picard/fastqtosam/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/fastqtosam/environment.yml +++ b/modules/nf-core/picard/fastqtosam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index dedd70a0318..f44aa16c78a 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -4,8 +4,8 @@ process PICARD_FASTQTOSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap index 2f999dcc9c9..69e952739ca 100644 --- a/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap +++ b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap @@ -3,39 +3,39 @@ "content": [ "e3cfa46b13cc4fc425cccae944f43b10", [ - "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + "versions.yml:md5,6a1888e4186ca3d82bd4d74ee677094c" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:50:01.762254" + "timestamp": "2024-10-18T11:04:07.175501513" }, "test-picard-fastqtosam-single": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + "versions.yml:md5,6a1888e4186ca3d82bd4d74ee677094c" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:49:32.460549" + "timestamp": "2024-10-18T11:03:34.501608306" }, "test-picard-fastqtosam-paired": { "content": [ "e3cfa46b13cc4fc425cccae944f43b10", [ - "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + "versions.yml:md5,6a1888e4186ca3d82bd4d74ee677094c" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:49:47.018269" + "timestamp": "2024-10-18T11:03:53.864451058" } } \ No newline at end of file diff --git a/modules/nf-core/picard/filtersamreads/environment.yml b/modules/nf-core/picard/filtersamreads/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/filtersamreads/environment.yml +++ b/modules/nf-core/picard/filtersamreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index 32977bdc306..7d0147e5c93 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -4,8 +4,8 @@ process PICARD_FILTERSAMREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/filtersamreads/tests/main.nf.test b/modules/nf-core/picard/filtersamreads/tests/main.nf.test new file mode 100644 index 00000000000..3cdde655c89 --- /dev/null +++ b/modules/nf-core/picard/filtersamreads/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process PICARD_FILTERSAMREADS" + script "../main.nf" + process "PICARD_FILTERSAMREADS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/filtersamreads" + tag "picard/sortsam" + + setup { + run("PICARD_SORTSAM") { + script "../../../picard/sortsam/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) + ] + input[1] = 'queryname' + """ + } + } + } + + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = PICARD_SORTSAM.out.bam.map{[ it[0], it[1], [] ]} + input[1] = 'includeAligned' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() } + ) + } + } + + test("sarscov2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] = PICARD_SORTSAM.out.bam.map{[ it[0], it[1], [] ]} + input[1] = 'includeAligned' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 - bam - readlist") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt', checkIfExists: true) + ] + input[1] = 'includeReadList' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() } + ) + } + } + + test("sarscov2 - bam - readlist - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt', checkIfExists: true) + ] + input[1] = 'includeReadList' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/picard/filtersamreads/tests/main.nf.test.snap b/modules/nf-core/picard/filtersamreads/tests/main.nf.test.snap new file mode 100644 index 00000000000..437239dedc5 --- /dev/null +++ b/modules/nf-core/picard/filtersamreads/tests/main.nf.test.snap @@ -0,0 +1,102 @@ +{ + "sarscov2 - bam - readlist - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:57:21.286660977" + }, + "sarscov2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:56:49.461946443" + }, + "sarscov2 - bam - readlist": { + "content": [ + "3c2a0fcd376bd70060073cb361fe91c1", + [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:57:05.707924464" + }, + "sarscov2 - bam": { + "content": [ + "b9847fed94d2b7286e18caaa099658ce", + [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:56:32.776141481" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/picard/filtersamreads/nextflow.config b/modules/nf-core/picard/filtersamreads/tests/nextflow.config similarity index 62% rename from tests/modules/nf-core/picard/filtersamreads/nextflow.config rename to modules/nf-core/picard/filtersamreads/tests/nextflow.config index 653e9633291..27844058124 100644 --- a/tests/modules/nf-core/picard/filtersamreads/nextflow.config +++ b/modules/nf-core/picard/filtersamreads/tests/nextflow.config @@ -1,13 +1,8 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: PICARD_SORTSAM { ext.prefix = { "${meta.id}.sorted" } } - withName: PICARD_FILTERSAMREADS { ext.prefix = { "${meta.id}.filtered" } } - } diff --git a/modules/nf-core/picard/fixmateinformation/environment.yml b/modules/nf-core/picard/fixmateinformation/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/fixmateinformation/environment.yml +++ b/modules/nf-core/picard/fixmateinformation/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index bf29e24cc07..2c075b8c69b 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -4,8 +4,8 @@ process PICARD_FIXMATEINFORMATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap index 799173a6f92..fb9e08afcd3 100644 --- a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap +++ b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "ddd0dc8f0cf1996d19dae51681187114", [ - "versions.yml:md5,36a59533c3e8578b046c4c2ec9caa8d4" + "versions.yml:md5,309cc65dc7918a6f1d81f5e0cf9455e4" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:45:26.092108" + "timestamp": "2024-10-18T10:23:11.403813574" } } \ No newline at end of file diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/liftovervcf/environment.yml +++ b/modules/nf-core/picard/liftovervcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index a4b27c88e5f..69feb624ac0 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -4,8 +4,8 @@ process PICARD_LIFTOVERVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap index 585ea369e8b..e88aa9706dc 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap @@ -4,27 +4,27 @@ "test.lifted.vcf.gz", "test.unlifted.vcf.gz", [ - "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91" + "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:38:05.840798" + "timestamp": "2024-10-18T12:08:23.913395641" }, "test-picard-liftovervcf": { "content": [ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", "39a9de5185d94289283bd27cfcdeba97", [ - "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91" + "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:41:33.022998" + "timestamp": "2024-10-18T12:08:12.803193917" } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index cf18ac35ca9..8a2ed64e6a6 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,8 +4,8 @@ process PICARD_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 8b37e65b1bc..13770a8e2e1 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -27,7 +27,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -54,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:32.025869" + "timestamp": "2024-10-18T10:58:50.046420643" }, "sarscov2 [unsorted bam] - stub": { "content": [ @@ -92,7 +92,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -119,69 +119,69 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:20.497105" + "timestamp": "2024-10-18T10:58:36.738907079" }, "sarscov2 [unsorted bam]": { "content": [ "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:50:14.881666" + "timestamp": "2024-10-18T10:57:16.683233382" }, "sarscov2 [sorted bam]": { "content": [ "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:52:03.11428" + "timestamp": "2024-10-18T10:57:47.416956759" }, "homo_sapiens [cram]": { "content": [ "test.marked.cram", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:53:05.403139" + "timestamp": "2024-10-18T10:58:15.143314223" }, "homo_sapiens [cram] - stub": { "content": [ @@ -211,7 +211,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -238,14 +238,14 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:43.438188" + "timestamp": "2024-10-18T10:59:03.402916523" } } \ No newline at end of file diff --git a/modules/nf-core/picard/mergesamfiles/environment.yml b/modules/nf-core/picard/mergesamfiles/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/mergesamfiles/environment.yml +++ b/modules/nf-core/picard/mergesamfiles/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 1e6e2274b9f..435339c63c9 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -4,8 +4,8 @@ process PICARD_MERGESAMFILES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap index 22d2331e46a..fe621300329 100644 --- a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap +++ b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "730da54c088350ff625d34b95e623dca", [ - "versions.yml:md5,3b5243ec10606330dd11a38fa7c7fa1f" + "versions.yml:md5,ba6df729752dd204080f8580ea5420c5" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T10:50:00.555746" + "timestamp": "2024-10-18T10:18:37.724686799" } } \ No newline at end of file diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/renamesampleinvcf/environment.yml +++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 3e4f38caa3c..9e5e2e2dc60 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -5,8 +5,8 @@ process PICARD_RENAMESAMPLEINVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap index a9bf7b7bf04..6a21666ad2d 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "e21a2349f41663d1fc38f47fbe65a6d5", [ - "versions.yml:md5,d4de734264e0c3b33d23e4a40de26a5f" + "versions.yml:md5,89be4b901aa05e78d449d11b00eff5e9" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:32:02.18878" + "timestamp": "2024-10-18T09:53:47.55538945" } } \ No newline at end of file diff --git a/modules/nf-core/picard/scatterintervalsbyns/environment.yml b/modules/nf-core/picard/scatterintervalsbyns/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/environment.yml +++ b/modules/nf-core/picard/scatterintervalsbyns/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/scatterintervalsbyns/main.nf b/modules/nf-core/picard/scatterintervalsbyns/main.nf index 344284804a1..fa5c7b145ff 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/main.nf +++ b/modules/nf-core/picard/scatterintervalsbyns/main.nf @@ -4,8 +4,8 @@ process PICARD_SCATTERINTERVALSBYNS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap b/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap index e08dff68334..68393dfefac 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap +++ b/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ], "intervals": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-27T10:31:47.186455" + "timestamp": "2024-10-18T11:09:20.872478896" }, "test-picard-scatterintervalsbyns": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ], "intervals": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:25:45.447792" + "timestamp": "2024-10-18T11:08:57.399354562" } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortsam/environment.yml b/modules/nf-core/picard/sortsam/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/sortsam/environment.yml +++ b/modules/nf-core/picard/sortsam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index af23e294bed..e3f4945d5b5 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -4,8 +4,8 @@ process PICARD_SORTSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test.snap b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap index bf447b8d135..22728f45d55 100644 --- a/modules/nf-core/picard/sortsam/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "b9847fed94d2b7286e18caaa099658ce", [ - "versions.yml:md5,f53876b7c58b5aa1564606f3c9c34108" + "versions.yml:md5,b1d858b31471d4a0ce2407c491b6e299" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:23:48.485054" + "timestamp": "2024-10-18T10:09:43.110521445" } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortvcf/environment.yml b/modules/nf-core/picard/sortvcf/environment.yml index ff4a85edb5f..1d715d564e9 100644 --- a/modules/nf-core/picard/sortvcf/environment.yml +++ b/modules/nf-core/picard/sortvcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 7133c13ae0c..a094e6bfae7 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -4,8 +4,8 @@ process PICARD_SORTVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap index db80323bfe5..e4a02c4f3e2 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap @@ -9,13 +9,13 @@ "##INFO=" ], [ - "versions.yml:md5,11949a1af95080dcc5bd1c75d68dee71" + "versions.yml:md5,e6e6356d3b5b1b8e8cfd5d4958c694e6" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:20:13.124551" + "timestamp": "2024-10-18T10:45:30.685264704" } } \ No newline at end of file diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index 471164faadc..b3f75777e46 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index e755d9a344f..3d653c0d08e 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -4,8 +4,8 @@ process SALMON_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: path genome_fasta diff --git a/modules/nf-core/salmon/index/tests/main.nf.test.snap b/modules/nf-core/salmon/index/tests/main.nf.test.snap index 703e455c574..e5899b51151 100644 --- a/modules/nf-core/salmon/index/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/index/tests/main.nf.test.snap @@ -2,25 +2,25 @@ "versions": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-22T14:26:33.32036" + "timestamp": "2024-10-18T10:00:47.087293189" }, "versions stub": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-23T09:47:58.828124" + "timestamp": "2024-10-18T10:01:03.89824494" } } \ No newline at end of file diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 471164faadc..b3f75777e46 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 6c528b24091..f1e3b5cda31 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -4,8 +4,8 @@ process SALMON_QUANT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test.snap b/modules/nf-core/salmon/quant/tests/main.nf.test.snap index 547ce2de1e0..ea22a80ce98 100644 --- a/modules/nf-core/salmon/quant/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/quant/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2 - single_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -15,15 +15,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:22.424672" + "timestamp": "2024-10-18T10:01:16.989080539" }, "sarscov2 - single_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -36,15 +36,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:32.292277" + "timestamp": "2024-10-18T10:01:29.340996235" }, "sarscov2 - single_end lib type A": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -57,15 +57,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:42.656382" + "timestamp": "2024-10-18T10:01:43.056167576" }, "sarscov2 - pair_end multiple": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -78,15 +78,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:33.03647" + "timestamp": "2024-10-18T10:03:05.500792631" }, "sarscov2 - pair_end multiple stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -99,15 +99,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:43.388379" + "timestamp": "2024-10-18T10:03:26.428959203" }, "sarscov2 - single_end lib type A stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -120,15 +120,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:52.612664" + "timestamp": "2024-10-18T10:02:03.420850208" }, "sarscov2 - pair_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -141,15 +141,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:05.577881" + "timestamp": "2024-10-18T10:02:16.130074696" }, "sarscov2 - pair_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -162,9 +162,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:15.286461" + "timestamp": "2024-10-18T10:02:39.470004547" } } \ No newline at end of file diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 0556de41a75..906b7486c0e 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stringtie=2.2.1 + - bioconda::stringtie=2.2.3 diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 6e25ba27d54..4635c8c5b13 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -4,8 +4,8 @@ process STRINGTIE_STRINGTIE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'biocontainers/stringtie:2.2.1--hecb563c_2' }" + 'https://depot.galaxyproject.org/singularity/stringtie:2.2.3--h43eeafb_0' : + 'biocontainers/stringtie:2.2.3--h43eeafb_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap index 124dd4cbe1c..d4645de3ee2 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -31,18 +31,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + "test.transcripts.gtf:md5,37154e7bda96544f24506ee902bb561d" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:44.299962" + "timestamp": "2024-10-18T09:56:50.294157199" }, "sarscov2 [bam] - forward strandedness": { "content": [ @@ -61,18 +61,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + "test.transcripts.gtf:md5,6087dfc9700a52d9e4a1ae3fcd1d1dfd" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:35.177738" + "timestamp": "2024-10-18T09:56:39.4249133" }, "sarscov2 [bam] - forward strandedness - stub": { "content": [ @@ -114,7 +114,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -153,15 +153,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:32.885078" + "timestamp": "2024-10-18T09:57:23.008470065" }, "sarscov2 [bam] - forward strandedness + reference annotation - stub": { "content": [ @@ -203,7 +203,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -242,15 +242,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:43.325777" + "timestamp": "2024-10-18T09:57:33.622824981" }, "sarscov2 [bam] - reverse strandedness + reference annotation - stub": { "content": [ @@ -292,7 +292,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -331,15 +331,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:37:06.085936" + "timestamp": "2024-10-18T09:57:55.803421433" }, "sarscov2 [bam] - reverse strandedness - stub": { "content": [ @@ -381,7 +381,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -420,15 +420,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:53.837578" + "timestamp": "2024-10-18T09:57:44.825389635" }, "sarscov2 [bam] - reverse strandedness + reference annotation": { "content": [ @@ -462,18 +462,18 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + "test.transcripts.gtf:md5,fbabb4e3888bbede67f11f692e484880" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:34:03.114695" + "timestamp": "2024-10-18T09:57:11.793664242" }, "sarscov2 [bam] - reverse strandedness": { "content": [ @@ -492,17 +492,17 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + "test.transcripts.gtf:md5,01d6da00a3c458420841e57427297183" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:52.874479" + "timestamp": "2024-10-18T09:57:01.166309777" } } \ No newline at end of file diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 7e919aa3177..fdb57502009 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread=2.0.1 + - bioconda::subread=2.0.6 diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 471bd16fd8d..d51de1e0b66 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -4,8 +4,8 @@ process SUBREAD_FEATURECOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : - 'biocontainers/subread:2.0.1--hed695b0_0' }" + 'https://depot.galaxyproject.org/singularity/subread:2.0.6--he4a0461_2' : + 'biocontainers/subread:2.0.6--he4a0461_2' }" input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap index 72e8dcddfdf..5a743f0ce3a 100644 --- a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap @@ -8,15 +8,15 @@ "single_end": true, "strandedness": "forward" }, - "test.featureCounts.txt:md5,0012df4c0a0e47eec1440017ab34f75f" + "test.featureCounts.txt:md5,4cf89f0e702ba9abef3fa571e68fe8f0" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.685863663" + "timestamp": "2024-10-18T10:19:47.695388295" }, "unstranded_counts": { "content": [ @@ -27,15 +27,15 @@ "single_end": true, "strandedness": "unstranded" }, - "test.featureCounts.txt:md5,3307d31b44a5d6bb3389786bb8f4e91f" + "test.featureCounts.txt:md5,c4ef2c2a80547fbb3074331bc0a1bda3" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.67903701" + "timestamp": "2024-10-18T10:21:03.208334705" }, "reverse_summary": { "content": [ @@ -80,7 +80,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -103,15 +103,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:22.628032" + "timestamp": "2024-10-18T10:20:10.040191252" }, "sarscov2 [bam] - reverse - stub": { "content": [ @@ -137,7 +137,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -160,15 +160,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:52.371212" + "timestamp": "2024-10-18T10:20:42.708101743" }, "reverse_counts": { "content": [ @@ -179,15 +179,15 @@ "single_end": true, "strandedness": "reverse" }, - "test.featureCounts.txt:md5,8175816b8260ed444d59232bd7e7120b" + "test.featureCounts.txt:md5,a7d8843ebc12d855c2e68d3e2e137582" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.160010804" + "timestamp": "2024-10-18T10:20:24.490755916" }, "sarscov2 [bam] - unstranded - stub": { "content": [ @@ -213,7 +213,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -236,15 +236,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:05:25.058902" + "timestamp": "2024-10-18T10:21:19.244837771" }, "forward_summary": { "content": [ @@ -268,14 +268,14 @@ "forward_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.704797013" + "timestamp": "2024-10-18T10:19:48.001158764" }, "unstranded_summary": { "content": [ @@ -299,25 +299,25 @@ "reverse_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.175265594" + "timestamp": "2024-10-18T10:20:24.551053149" }, "unstranded_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.69390501" + "timestamp": "2024-10-18T10:21:03.25895568" } } \ No newline at end of file diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index f172c1b39e9..910ffa882f5 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::cutadapt=3.4 - - bioconda::trim-galore=0.6.7 + - bioconda::cutadapt=4.2 + - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 0e2f32902bc..30d17edc176 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 6cb31c9f9d2..61b3504a991 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:20.401347" + "timestamp": "2024-10-18T12:50:36.440264431" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -77,10 +77,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:27:44.964166" + "timestamp": "2024-10-18T12:50:51.25902234" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -160,21 +160,21 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:28:07.611496" + "timestamp": "2024-10-18T12:51:19.024228479" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:28.960497" + "timestamp": "2024-10-18T12:51:02.471703095" } } \ No newline at end of file diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index a54fb8f1654..27868a444c5 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedgraphtobigwig=445 + - bioconda::ucsc-bedgraphtobigwig=469 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index bff0b00a93a..81cdee95326 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -5,8 +5,8 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:445--h954228d_0' : - 'biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0' }" + 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:469--h9b8f530_0' : + 'biocontainers/ucsc-bedgraphtobigwig:469--h9b8f530_0' }" input: tuple val(meta), path(bedgraph) @@ -22,7 +22,7 @@ process UCSC_BEDGRAPHTOBIGWIG { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ bedGraphToBigWig \\ $bedgraph \\ @@ -37,7 +37,7 @@ process UCSC_BEDGRAPHTOBIGWIG { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.bigWig diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap index 7b018158313..7c731f65102 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:06:05.176746" + "timestamp": "2024-10-18T10:47:58.558813949" }, "Should run without failures": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:05:56.658148" + "timestamp": "2024-10-18T10:47:36.476844229" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index 093d9c8c396..50ecf675d12 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - cram": { "content": [ "test.cram", - "test.cram.crai:md5,cb5268070f99cdd0d86f43613e5fc7db", + "test.cram.crai:md5,9a74bf028b7146d8ef285442a14bbc8f", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", "test.stats:md5,1a4569080c6f73546a863b0c3bc72c49", @@ -10,7 +10,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], @@ -18,7 +18,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:06:04.991702832" + "timestamp": "2024-10-18T10:59:53.440891602" }, "sarscov2 - bam - stub": { "content": [ @@ -90,7 +90,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -160,7 +160,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } @@ -169,7 +169,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:06:20.672273462" + "timestamp": "2024-10-18T11:00:20.860494683" }, "homo_sapiens - cram - stub": { "content": [ @@ -235,7 +235,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -299,7 +299,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } @@ -308,12 +308,12 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:06:36.739909544" + "timestamp": "2024-10-18T11:00:42.042387118" }, "sarscov2 - bam": { "content": [ - "test.bam:md5,d1a53820e4a6e42ca8aceab51d74cf57", - "test.bam.bai:md5,be9485a644813773fb893a0a6b9b977c", + "test.bam:md5,c8a3a56d56bf2c87f09e143ed2f78a7d", + "test.bam.bai:md5,7d205e4e0b3d98887b1eafb5c50a3363", "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", "test.stats:md5,ba007b13981dad548358c7c957d41e12", @@ -321,7 +321,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], @@ -329,6 +329,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:05:46.507645441" + "timestamp": "2024-10-18T10:59:22.840531827" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap index f02de25e29c..d3e8656a46a 100644 --- a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap @@ -57,15 +57,15 @@ "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,d61a29a9b3d8c60ed90b068df8032979", - "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d" + "versions.yml:md5,92450dccc1a141f405d689d7f07480c0", + "versions.yml:md5,df149b65b51dcad73b8914e6ce30fadf" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:38:29.298437201" + "timestamp": "2024-10-18T10:16:09.107786306" }, "sascov2_wgs - [bam,bai]": { "content": [ @@ -114,14 +114,14 @@ "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d", - "versions.yml:md5,ebe92bff64a6e7b1a0aa741674d24893" + "versions.yml:md5,21d43bb86ef743e75e729dfa77ba8f91", + "versions.yml:md5,92450dccc1a141f405d689d7f07480c0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:38:09.338919835" + "timestamp": "2024-10-18T10:15:48.344077986" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap index 26ed39c00a7..7bbcf72b7cb 100644 --- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ], "bedgraph": [ @@ -43,16 +43,16 @@ ] ], "versions": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-26T01:55:31.016058335" + "timestamp": "2024-10-18T10:48:23.095911334" }, "sarscov2 [bedgraph] [genome_sizes] - stub": { "content": [ @@ -76,7 +76,7 @@ ] ], "2": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ], "bedgraph": [ @@ -98,15 +98,15 @@ ] ], "versions": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:22:51.388076" + "timestamp": "2024-10-18T10:48:45.587883209" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index 46bf3acf29e..f8a746aa6b5 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -60,8 +60,8 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -122,17 +122,17 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:34.919444" + "timestamp": "2024-10-18T12:18:56.222595833" }, "test paired end read without UMI - stub": { "content": [ @@ -192,7 +192,7 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -250,16 +250,16 @@ ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:51.765414" + "timestamp": "2024-10-18T12:19:07.775855857" }, "test paired end read without UMI": { "content": [ @@ -288,15 +288,15 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:37.366404" + "timestamp": "2024-10-18T12:18:19.621101515" }, "test single end read with UMI": { "content": [ @@ -322,16 +322,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:04:53.072227" + "timestamp": "2024-10-18T12:17:51.049984482" }, "test paired end read with UMI": { "content": [ @@ -357,16 +357,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:16.709704" + "timestamp": "2024-10-18T12:18:07.106739839" }, "test skip all steps": { "content": [ @@ -447,8 +447,8 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -509,16 +509,16 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:09.844235" + "timestamp": "2024-10-18T12:18:42.513733457" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap index e0c944f3157..f7e64e1f362 100644 --- a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap @@ -30,14 +30,14 @@ ], [ "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:35.832206" + "timestamp": "2024-10-18T10:04:10.67385556" }, "homo_sapiens paired-end [fastq] - stub": { "content": [ @@ -104,7 +104,7 @@ ], "5": [ "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c" ], "index": [ [ @@ -168,14 +168,14 @@ ], "versions": [ "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:56.819" + "timestamp": "2024-10-18T10:04:26.972793491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap index 4db35cced7f..9c49c151375 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap @@ -54,17 +54,17 @@ ] ], [ - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:19.861809" + "timestamp": "2024-10-18T10:06:55.431718491" }, "salmon - stub": { "content": [ @@ -122,9 +122,9 @@ ] ], "14": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ], "2": [ @@ -308,18 +308,18 @@ ] ], "versions": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:55.281379" + "timestamp": "2024-10-18T10:07:30.425544183" }, "kallisto - stub": { "content": [ @@ -375,7 +375,7 @@ ] ], "14": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" @@ -559,7 +559,7 @@ ] ], "versions": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" @@ -567,10 +567,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:37:29.239014" + "timestamp": "2024-10-18T10:08:20.127524239" }, "salmon": { "content": [ @@ -629,16 +629,16 @@ ] ], [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:35:48.954002" + "timestamp": "2024-10-18T10:06:18.517305145" } } \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e40cb75442f..596b04c8d8c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -512,12 +512,6 @@ paragraph/multigrmpy: phyloflash: - modules/nf-core/phyloflash/** - tests/modules/nf-core/phyloflash/** -picard/collectrnaseqmetrics: - - modules/nf-core/picard/collectrnaseqmetrics/** - - tests/modules/nf-core/picard/collectrnaseqmetrics/** -picard/filtersamreads: - - modules/nf-core/picard/filtersamreads/** - - tests/modules/nf-core/picard/filtersamreads/** plink/exclude: - modules/nf-core/plink/exclude/** - tests/modules/nf-core/plink/exclude/** diff --git a/tests/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/tests/modules/nf-core/picard/collectrnaseqmetrics/main.nf deleted file mode 100644 index a53d7bbeecb..00000000000 --- a/tests/modules/nf-core/picard/collectrnaseqmetrics/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UCSC_GTFTOGENEPRED } from '../../../../../modules/nf-core/ucsc/gtftogenepred/main.nf' -include { PICARD_COLLECTRNASEQMETRICS } from '../../../../../modules/nf-core/picard/collectrnaseqmetrics/main.nf' - -workflow test_picard_collectrnaseqmetrics { - - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - - input_gtftogenepred = [ - [ id:'test'], - gtf - ] - - UCSC_GTFTOGENEPRED(input_gtftogenepred) - - input_collectrnaseqmetrics = [ - [ id:'test', single_end:false, strandedness:'forward' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - PICARD_COLLECTRNASEQMETRICS( - input_collectrnaseqmetrics, - UCSC_GTFTOGENEPRED.out.refflat.map{ it[1] }, - fasta, - [] - ) - -} diff --git a/tests/modules/nf-core/picard/collectrnaseqmetrics/test.yml b/tests/modules/nf-core/picard/collectrnaseqmetrics/test.yml deleted file mode 100644 index 01289cb93a1..00000000000 --- a/tests/modules/nf-core/picard/collectrnaseqmetrics/test.yml +++ /dev/null @@ -1,15 +0,0 @@ -- name: picard collectrnaseqmetrics test_picard_collectrnaseqmetrics - command: nextflow run ./tests/modules/nf-core/picard/collectrnaseqmetrics -entry test_picard_collectrnaseqmetrics -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config - tags: - - picard - - picard/collectrnaseqmetrics - files: - - path: output/picard/test.rna_metrics - contains: - - "CollectRnaSeqMetrics" - - path: output/picard/versions.yml - - path: output/ucsc/test.genepred - md5sum: 779e4749efaf38da3443ddfde30cc76c - - path: output/ucsc/test.refflat - md5sum: 4101802f41d4cf7ee2667587da11bf42 - - path: output/ucsc/versions.yml diff --git a/tests/modules/nf-core/picard/filtersamreads/main.nf b/tests/modules/nf-core/picard/filtersamreads/main.nf deleted file mode 100644 index 3687bbfb19b..00000000000 --- a/tests/modules/nf-core/picard/filtersamreads/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf' -include { PICARD_FILTERSAMREADS } from '../../../../../modules/nf-core/picard/filtersamreads/main.nf' - -workflow test_picard_filtersamreads { - - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ] - sort_order = 'queryname' - filter = 'includeAligned' - - PICARD_SORTSAM ( input, sort_order ) - PICARD_SORTSAM.out.bam - .map { - [ it[0], it[1], [] ] - } - .set{ ch_sorted_for_filtersamreads } - PICARD_FILTERSAMREADS ( ch_sorted_for_filtersamreads, filter ) -} - -workflow test_picard_filtersamreads_readlist { - - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_single_end_bam_readlist_txt'], checkIfExists: true) ] - filter = 'includeReadList' - - PICARD_FILTERSAMREADS ( input, filter ) -} diff --git a/tests/modules/nf-core/picard/filtersamreads/test.yml b/tests/modules/nf-core/picard/filtersamreads/test.yml deleted file mode 100644 index 1404960b665..00000000000 --- a/tests/modules/nf-core/picard/filtersamreads/test.yml +++ /dev/null @@ -1,30 +0,0 @@ -- name: picard filtersamreads test_picard_filtersamreads - command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config - tags: - - picard - - picard/filtersamreads - files: - - path: output/picard/test.filtered.bam - md5sum: b44a6ca04811a9470c7813c3c9465fd5 - - path: output/picard/test.sorted.bam - md5sum: b44a6ca04811a9470c7813c3c9465fd5 - - path: output/picard/versions.yml - -- name: picard filtersamreads test_picard_filtersamreads_readlist - command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config - tags: - - picard - - picard/filtersamreads - files: - - path: output/picard/test.filtered.bam - md5sum: 1e86b738b56f2c2b09f4cab52baf05c7 - - path: output/picard/versions.yml - -- name: picard filtersamreads test_picard_filtersamreads_readlist stub - command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config -stub-run - tags: - - picard - - picard/filtersamreads - files: - - path: output/picard/test.filtered.bam - - path: output/picard/versions.yml