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New module: checkqc #4158
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New module: checkqc #4158
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438d3b4
Add template module with nf-core with some modifications
matrulda 7b2dbbf
checkqc: Removed TODOs, added tests (need improvement), copy files wh…
matrulda 90538df
Use nf-tests for checkQC
matrulda dc76d6f
Change logic of mitohifi/mitohifi api (#4193)
ksenia-krasheninnikova 7e2e138
Sentieon/tnfilter (#4208)
asp8200 d2c747d
pycoqc: add nf-test (#4238)
koenbossers 7c4ffb4
Update seqkit/fx2tab to version 2.5.1 (#4240)
heuermh 5de8431
FEAT: update bclconvert to 4.2.4 (#4253)
maxulysse c54c9d5
Add conda to renovate (#4216)
edmundmiller 67aeaf5
chore(deps): update pre-commit hook python-jsonschema/check-jsonschem…
renovate[bot] a97fbad
chore(deps): update pre-commit hook pre-commit/mirrors-prettier to v3…
renovate[bot] 26954e9
Fix conda declaration (#4252)
nvnieuwk 3fd1004
chore(config): migrate renovate config (#4255)
renovate[bot] 7a57477
chore(deps): update docker.io/continuumio/miniconda3 docker tag to v2…
renovate[bot] 4805ef1
Fix linting test not being run for modules with only nf-test tests (#…
nvnieuwk 9799d88
Nf-test rtgtools/rocplot (#4200)
nvnieuwk d307124
samtools/merge - emit crai file when cram file created (#4258)
gq1 1e5d77c
chore(deps): update biocontainers/chromap docker tag to v0.2.5 (#4214)
renovate[bot] c126028
Use "error" rather than "exit 1", and removed `quay.io/` (#4248)
muffato 08604d0
chore(deps): update biocontainers/goat docker tag to v0.2.5 (#4259)
renovate[bot] 10d6fa4
change database sufix to nin which is more common in v5 and v4 databa…
yumisims a3917ee
add nf-tests and snapshots for kallisto index & quant (#4250)
sateeshperi 230f8a0
Update genomescope (#4267)
mahesh-panchal d133bca
nf-test interproscan (#4269)
vagkaratzas b9813bb
Update busco (#4270)
mahesh-panchal 15815c7
chore(deps): update biocontainers/bowtie2 docker tag to v2.4.5 (#4212)
renovate[bot] eda0bd0
chore(deps): update biocontainers/checkm-genome docker tag to v1.2.2 …
renovate[bot] b9085d6
Mitohifi channel input (#4254)
ksenia-krasheninnikova 2fee75d
chore(deps): Bump checkm-genome conda env (#4279)
edmundmiller 689ed92
chore(deps): update biocontainers/htseq docker tag to v2.0.3 (#4266)
renovate[bot] 77d971c
Fix up kallisto (#4271)
pinin4fjords f6c9cc8
FIX: More coherence in all gatk4spark modules (#4282)
maxulysse 95332f6
update multiqc to 1.17 in custom/dumpsoftwareversions (#4295)
maxulysse 3bd6b8f
Rename utility subworkflows (#4268)
adamrtalbot b601d83
Ucsc/bedgraphtobigwig nftest (#4136)
laramiellindsey 89b54cf
Update missed renovate environments (#4296)
edmundmiller 5256c9f
build: Add renovate comments to conda packages (#4298)
edmundmiller d9e2001
Fix conda and renovate (#4299)
edmundmiller 46c5d28
Add renovate config check (#4297)
edmundmiller dd55c30
add arriba download (#4280)
peterpru 1c0d47d
add agat/convertspgff2tsv module (#4265)
rannick c98065d
Bug: nf-test bam_sort_stats_samtools (#4190)
Joon-Klaps e87c53d
new module gridss GeneratePonBedpe (#4196)
kubranarci 15068f2
3167 new module gridss gridss somatic filter (#4247)
kubranarci 0bddc14
Added a meta map for the reference genome of minimap2 (#4285)
muffato 0729b51
Add ngscheckmate bed file to test_data config (#4308)
SPPearce 62322e3
Diamond tools: nf-test, container update, stubs added, makedb meta ad…
vagkaratzas f1f3a5f
blastp added choice for xml or tsv outputs other than the existing cs…
vagkaratzas ddff74a
Apply suggestions from code review
matrulda 107dab6
Remove trailing white space
matrulda 0e8d1eb
Merge branch 'master' into checkqc
matrulda f749839
Apply suggestions from code review
matrulda 0ffb054
Handle Failed QC and add test for it
matrulda 32e1808
Update modules/nf-core/checkqc/main.nf
matrulda c2ca108
Update modules/nf-core/checkqc/main.nf
matrulda 51e3636
Update to CheckQC v4.0.1
matrulda 55e9b98
Address lint errors and warnings
matrulda 43d6d21
Merge branch 'master' into checkqc
matrulda 048260b
Merge branch 'master' into checkqc
nvnieuwk 3f660a0
update main.nf.test to new guidelines
nvnieuwk 9789f75
using an env.yaml for conda
nvnieuwk 7f2aeca
Merge branch 'master' into checkqc
SPPearce c9734d3
Merge branch 'master' into checkqc
fmalmeida 659759a
add community wave container
atrigila e441e06
update snapshot
atrigila 782454a
remove conda config
atrigila d30a189
add metamap
atrigila 7eaf61a
update test and snapshot
atrigila fae13f3
Merge branch 'master' into checkqc
atrigila 48da3f9
Merge branch 'master' into checkqc
fmalmeida 5b584d8
add yml for tracking versions
atrigila 70f9b8f
skip checkqc conda profile
fmalmeida 0d07bfd
fix linting
atrigila d9b2e91
Update test.yml
maxulysse ba7bc1b
Update .github/workflows/test.yml
maxulysse d13ce00
Merge branch 'master' into checkqc
maxulysse 0e9516f
Merge branch 'master' into checkqc
atrigila d2cc55d
add fixme note as requested in slack
atrigila 80bdbac
Merge branch 'master' into checkqc
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process CHECKQC { | ||
label 'process_single' | ||
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conda "bioconda::checkqc=4.0.1=pyhdfd78af_0" | ||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
'https://depot.galaxyproject.org/singularity/checkqc:4.0.1--pyhdfd78af_0': | ||
'biocontainers/checkqc:4.0.1--pyhdfd78af_0' }" | ||
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input: | ||
path(run_dir) | ||
path(checkqc_config) | ||
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output: | ||
path "*checkqc_report.json", emit: report | ||
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path "versions.yml" , emit: versions | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
def args = task.ext.args ?: '' | ||
def config = checkqc_config ? "--config $checkqc_config" : '' | ||
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""" | ||
checkqc \ | ||
$args \ | ||
$config \ | ||
--json \ | ||
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$run_dir > checkqc_report.json || test -s "checkqc_report.json" | ||
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cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
checkqc: \$( checkqc --version | sed -e "s/checkqc, version //g" ) | ||
END_VERSIONS | ||
""" | ||
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stub: | ||
def args = task.ext.args ?: '' | ||
""" | ||
touch checkqc_report.json | ||
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cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
checkqc: \$( checkqc --version | sed -e "s/checkqc, version //g" ) | ||
END_VERSIONS | ||
""" | ||
} |
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Original file line number | Diff line number | Diff line change |
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--- | ||
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json | ||
name: "checkqc" | ||
description: A simple program to parse Illumina NGS data and check it for quality criteria | ||
keywords: | ||
- QC | ||
- Illumina | ||
- genomics | ||
tools: | ||
- "checkqc": | ||
description: "A simple program to parse Illumina NGS data and check it for quality criteria." | ||
homepage: "https://github.com/Molmed/checkQC" | ||
documentation: "http://checkqc.readthedocs.io/en/latest/" | ||
doi: "10.21105/joss.00556" | ||
licence: "['GPL v3']" | ||
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input: | ||
- run_dir: | ||
type: file | ||
description: | | ||
Illumina sequencing run directory | ||
Can be directory or a compressed tar (tar.gz) of the directory | ||
- checkqc_config: | ||
type: file | ||
description: CheckQC configuration file | ||
pattern: "*.{yml,yaml}" | ||
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output: | ||
- versions: | ||
type: file | ||
description: File containing software versions | ||
pattern: "versions.yml" | ||
- checkqc_report: | ||
type: file | ||
description: CheckQC report in json format | ||
pattern: "*checkqc_report.json" | ||
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authors: | ||
- "@matrulda" |
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Original file line number | Diff line number | Diff line change |
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nextflow_process { | ||
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name "Test Process CHECKQC" | ||
script "../main.nf" | ||
process "CHECKQC" | ||
tag "modules" | ||
tag "modules_nfcore" | ||
tag "checkqc" | ||
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test("homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC OK") { | ||
config "./test_checkqc.config" | ||
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setup { | ||
run("UNTAR") { | ||
script "../../untar/main.nf" | ||
process { | ||
""" | ||
input[0] = Channel.of([ [], file(params.test_data['homo_sapiens']['illumina']['test_interop_bcl2fastqstats_flowcell'], checkIfExists: true)]) | ||
""" | ||
} | ||
} | ||
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} | ||
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when { | ||
process { | ||
""" | ||
input[0] = UNTAR.out.untar.map{ it[1] } | ||
input[1] = [] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
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} | ||
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test("homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC FAIL") { | ||
config "./test_checkqc_fail.config" | ||
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setup { | ||
run("UNTAR") { | ||
script "../../untar/main.nf" | ||
process { | ||
""" | ||
input[0] = Channel.of([ [], file(params.test_data['homo_sapiens']['illumina']['test_interop_bcl2fastqstats_flowcell'], checkIfExists: true)]) | ||
""" | ||
} | ||
} | ||
} | ||
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when { | ||
process { | ||
""" | ||
input[0] = UNTAR.out.untar.map{ it[1] } | ||
input[1] = [] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
|
||
} | ||
|
||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,40 @@ | ||
{ | ||
"homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC FAIL": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
"checkqc_report.json:md5,0f27336ae332afe0791d0d3be0edb976" | ||
], | ||
"1": [ | ||
"versions.yml:md5,70db37623d836596a0264179eff546ab" | ||
], | ||
"report": [ | ||
"checkqc_report.json:md5,0f27336ae332afe0791d0d3be0edb976" | ||
], | ||
"versions": [ | ||
"versions.yml:md5,70db37623d836596a0264179eff546ab" | ||
] | ||
} | ||
], | ||
"timestamp": "2024-03-19T08:14:00.336789034" | ||
}, | ||
"homo_sapiens illumina test_interop_bcl2fastqstats_flowcell - QC OK": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
"checkqc_report.json:md5,c69cb912a8c5bf53544764bd5bd73ae5" | ||
], | ||
"1": [ | ||
"versions.yml:md5,70db37623d836596a0264179eff546ab" | ||
], | ||
"report": [ | ||
"checkqc_report.json:md5,c69cb912a8c5bf53544764bd5bd73ae5" | ||
], | ||
"versions": [ | ||
"versions.yml:md5,70db37623d836596a0264179eff546ab" | ||
] | ||
} | ||
], | ||
"timestamp": "2024-03-19T08:13:32.727679717" | ||
} | ||
} |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,2 @@ | ||
checkqc: | ||
- modules/nf-core/checkqc/** |
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process { | ||
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
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withName: CHECKQC { | ||
ext.args = '--downgrade-errors ReadsPerSampleHandler' | ||
} | ||
} |
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@@ -0,0 +1,8 @@ | ||
process { | ||
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
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withName: CHECKQC { | ||
ext.args = '' | ||
} | ||
} |
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Can you add a meta map here?