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Registry update for all modules #509

Merged
merged 7 commits into from
Sep 25, 2023
Merged

Registry update for all modules #509

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e7d9600
Update all URLs and modules except samtools/gtdbtk
jfy133 Sep 15, 2023
6b33f90
Fix porechop and start fixing aDNA samtools faidx fix
jfy133 Sep 15, 2023
c5ff72b
Merge branch '2.4-review-comments' into registry-update
jfy133 Sep 15, 2023
3205a96
Merge branch 'dev' into registry-update
jfy133 Sep 16, 2023
4b15996
Fix SAMTools FAIDX
jfy133 Sep 16, 2023
6ea1f62
Fix ancient DNA samtools FAIX channels and clean up freebayes input c…
jfy133 Sep 16, 2023
b8f07b9
Fix linting error (not tested!)
jfy133 Sep 16, 2023
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60 changes: 29 additions & 31 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
"nf-core": {
"adapterremoval": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"aria2": {
Expand All @@ -18,22 +18,22 @@
},
"bbmap/bbnorm": {
"branch": "master",
"git_sha": "c7f047d51b29a49aff34b86d059291ae43d1f296",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"bcftools/consensus": {
"branch": "master",
"git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bcftools/index": {
"branch": "master",
"git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bcftools/view": {
"branch": "master",
"git_sha": "fa12afdf5874c1d11e4a20efe81c97935e8eea24",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cat/fastq": {
Expand All @@ -43,12 +43,12 @@
},
"checkm/lineagewf": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"checkm/qa": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"concoct/concoct": {
Expand Down Expand Up @@ -78,45 +78,43 @@
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
"git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
"installed_by": ["modules"]
},
"dastool/dastool": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"dastool/fastatocontig2bin": {
"branch": "master",
"git_sha": "8ffb8ec8e49aafe43240b652147d70d56f150b3c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "20a508676f40d0fd3f911ac595af91ec845704c4",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
"installed_by": ["modules"]
},
"freebayes": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"genomad/download": {
"branch": "master",
"git_sha": "ca813f3f73adedf3547a5a677e992d9d43a71870",
"installed_by": ["modules"],
"patch": "modules/nf-core/genomad/download/genomad-download.diff"
"installed_by": ["modules"]
},
"genomad/endtoend": {
"branch": "master",
"git_sha": "ca813f3f73adedf3547a5a677e992d9d43a71870",
"installed_by": ["modules"],
"patch": "modules/nf-core/genomad/endtoend/genomad-endtoend.diff"
"installed_by": ["modules"]
},
"gtdbtk/classifywf": {
"branch": "master",
Expand All @@ -125,32 +123,32 @@
},
"gunc/downloaddb": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gunc/mergecheckm": {
"branch": "master",
"git_sha": "93f8308f6c1ef35b6b8cd264cefd22853fc51526",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gunc/run": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "38b16706fa3a9d4ee2bf46fa5805e7397e275cdd",
"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
"installed_by": ["modules"]
},
"maxbin2": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"metabat2/jgisummarizebamcontigdepths": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"metabat2/metabat2": {
Expand All @@ -170,42 +168,42 @@
},
"multiqc": {
"branch": "master",
"git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
"installed_by": ["modules"]
},
"prodigal": {
"branch": "master",
"git_sha": "8c4f2d2ceeb5e9cc4a49a91c0e9a675b6724c043",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"prokka": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"pydamage/analyze": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"pydamage/filter": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "371eff7748d769c2ddc8bd593773523a364a52fe",
"git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
"installed_by": ["modules"]
},
"seqtk/mergepe": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"tiara/tiara": {
"branch": "master",
"git_sha": "d91e3d3d4806179065b087b91ff36c11976bf233",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
}
}
Expand Down
2 changes: 1 addition & 1 deletion modules/local/adjust_maxbin2_ext.nf
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Expand Up @@ -6,7 +6,7 @@ process ADJUST_MAXBIN2_EXT {
conda "bioconda::multiqc=1.12"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
'biocontainers/multiqc:1.12--pyhdfd78af_0' }"

input:
tuple val(meta), path(bins)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bin_summary.nf
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Expand Up @@ -3,7 +3,7 @@ process BIN_SUMMARY {
conda "conda-forge::pandas=1.4.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
'quay.io/biocontainers/pandas:1.4.3' }"
'biocontainers/pandas:1.4.3' }"

input:
path(bin_depths)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bowtie2_assembly_align.nf
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Expand Up @@ -4,7 +4,7 @@ process BOWTIE2_ASSEMBLY_ALIGN {
conda "bioconda::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' :
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"
'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"

input:
tuple val(assembly_meta), path(assembly), path(index), val(reads_meta), path(reads)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bowtie2_assembly_build.nf
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Expand Up @@ -4,7 +4,7 @@ process BOWTIE2_ASSEMBLY_BUILD {
conda "bioconda::bowtie2=2.4.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1' :
'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
'biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"

input:
tuple val(meta), path(assembly)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bowtie2_removal_align.nf
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Expand Up @@ -7,7 +7,7 @@ process BOWTIE2_REMOVAL_ALIGN {
conda "bioconda::bowtie2=2.4.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1' :
'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
'biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"

input:
tuple val(meta), path(reads)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bowtie2_removal_build.nf
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Expand Up @@ -4,7 +4,7 @@ process BOWTIE2_REMOVAL_BUILD {
conda "bioconda::bowtie2=2.4.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1' :
'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"
'biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1' }"

input:
path fasta
Expand Down
2 changes: 1 addition & 1 deletion modules/local/busco.nf
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Expand Up @@ -4,7 +4,7 @@ process BUSCO {
conda "bioconda::busco=5.4.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0':
'quay.io/biocontainers/busco:5.4.3--pyhdfd78af_0' }"
'biocontainers/busco:5.4.3--pyhdfd78af_0' }"

input:
tuple val(meta), path(bin)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/busco_db_preparation.nf
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Expand Up @@ -4,7 +4,7 @@ process BUSCO_DB_PREPARATION {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'docker.io/ubuntu:20.04' }"
'nf-core/ubuntu:20.04' }"

input:
path database
Expand Down
2 changes: 1 addition & 1 deletion modules/local/busco_save_download.nf
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Expand Up @@ -5,7 +5,7 @@ process BUSCO_SAVE_DOWNLOAD {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'docker.io/ubuntu:20.04' }"
'nf-core/ubuntu:20.04' }"

input:
path(busco_downloads)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/busco_summary.nf
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Expand Up @@ -3,7 +3,7 @@ process BUSCO_SUMMARY {
conda "conda-forge::pandas=1.4.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
'quay.io/biocontainers/pandas:1.4.3' }"
'biocontainers/pandas:1.4.3' }"

input:
path(summaries_domain)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/cat.nf
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Expand Up @@ -4,7 +4,7 @@ process CAT {
conda "bioconda::cat=4.6 bioconda::diamond=2.0.6"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' :
'quay.io/biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"
'biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"

input:
tuple val(meta), path("bins/*")
Expand Down
2 changes: 1 addition & 1 deletion modules/local/cat_db.nf
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Expand Up @@ -4,7 +4,7 @@ process CAT_DB {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'docker.io/ubuntu:20.04' }"
'nf-core/ubuntu:20.04' }"

input:
path(database)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/cat_db_generate.nf
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Expand Up @@ -3,7 +3,7 @@ process CAT_DB_GENERATE {
conda "bioconda::cat=4.6 bioconda::diamond=2.0.6"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' :
'quay.io/biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"
'biocontainers/mulled-v2-75e2a26f10cbf3629edf2d1600db3fed5ebe6e04:eae321284604f7dabbdf121e3070bda907b91266-0' }"

output:
tuple env(DB_NAME), path("database/*"), path("taxonomy/*"), emit: db
Expand Down
2 changes: 1 addition & 1 deletion modules/local/cat_summary.nf
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Expand Up @@ -4,7 +4,7 @@ process CAT_SUMMARY {
conda "bioconda::bioawk=1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioawk:1.0--hed695b0_5' :
'quay.io/biocontainers/bioawk:1.0--hed695b0_5' }"
'biocontainers/bioawk:1.0--hed695b0_5' }"

input:
path(cat_summaries)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/centrifuge.nf
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Expand Up @@ -4,7 +4,7 @@ process CENTRIFUGE {
conda "bioconda::centrifuge=1.0.4_beta"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--he513fc3_5' :
'quay.io/biocontainers/centrifuge:1.0.4_beta--he513fc3_5' }"
'biocontainers/centrifuge:1.0.4_beta--he513fc3_5' }"

input:
tuple val(meta), path(reads)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/centrifuge_db_preparation.nf
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Expand Up @@ -3,7 +3,7 @@ process CENTRIFUGE_DB_PREPARATION {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'docker.io/ubuntu:20.04' }"
'nf-core/ubuntu:20.04' }"

input:
path db
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2 changes: 1 addition & 1 deletion modules/local/combine_tsv.nf
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Expand Up @@ -4,7 +4,7 @@ process COMBINE_TSV {
conda "bioconda::bioawk=1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioawk:1.0--hed695b0_5' :
'quay.io/biocontainers/bioawk:1.0--hed695b0_5' }"
'biocontainers/bioawk:1.0--hed695b0_5' }"

input:
path(bin_summaries)
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2 changes: 1 addition & 1 deletion modules/local/convert_depths.nf
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Expand Up @@ -4,7 +4,7 @@ process CONVERT_DEPTHS {
conda "bioconda::bioawk=1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioawk:1.0--hed695b0_5' :
'quay.io/biocontainers/bioawk:1.0--hed695b0_5' }"
'biocontainers/bioawk:1.0--hed695b0_5' }"

input:
tuple val(meta), path(fasta), path(depth)
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2 changes: 1 addition & 1 deletion modules/local/filtlong.nf
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Expand Up @@ -4,7 +4,7 @@ process FILTLONG {
conda "bioconda::filtlong=0.2.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/filtlong:0.2.0--he513fc3_3' :
'quay.io/biocontainers/filtlong:0.2.0--he513fc3_3' }"
'biocontainers/filtlong:0.2.0--he513fc3_3' }"

input:
tuple val(meta), path(long_reads), path(short_reads_1), path(short_reads_2)
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2 changes: 1 addition & 1 deletion modules/local/gtdbtk_db_preparation.nf
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Expand Up @@ -4,7 +4,7 @@ process GTDBTK_DB_PREPARATION {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'docker.io/ubuntu:20.04' }"
'nf-core/ubuntu:20.04' }"

input:
path(database)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/gtdbtk_summary.nf
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Expand Up @@ -4,7 +4,7 @@ process GTDBTK_SUMMARY {
conda "conda-forge::pandas=1.4.3"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
'quay.io/biocontainers/pandas:1.4.3' }"
'biocontainers/pandas:1.4.3' }"

input:
path(qc_discarded_bins)
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2 changes: 1 addition & 1 deletion modules/local/kraken2.nf
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Expand Up @@ -4,7 +4,7 @@ process KRAKEN2 {
conda "bioconda::kraken2=2.0.8_beta"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kraken2:2.0.8_beta--pl526hc9558a2_2' :
'quay.io/biocontainers/kraken2:2.0.8_beta--pl526hc9558a2_2' }"
'biocontainers/kraken2:2.0.8_beta--pl526hc9558a2_2' }"

input:
tuple val(meta), path(reads)
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