Dev #473
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added 8 commits
December 13, 2021 16:25
linting update publishDir linting
FriederikeHanssen
requested changes
Dec 13, 2021
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hey @nickhsmith thanks a lot for fixing the publish copy issue 😊 anything that is not right in nf-core/modules should be fixed in that repository, so we can properly pull from there. Since you have also adressed some of the null/false things in the nextflow.config here, maybe we can wait for conclusion on the discussion and Maxime to merge his PR. We could certainly add the things about Haplotypecaller here, and once Gavin is ready just overwrite it.
| ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last().concat('.')) : "${meta.id}" } | ||
| publishDir = [ |
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if it is not enabled, i don't think this needs to be here
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I like having the same format, and if someone decides tomorrow to output/publish this module. All they need to do is to change enabled But it's definitely not used now
| pattern: "*{bam,bai}" | ||
| ] | ||
| } | ||
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| withName: 'SAMTOOLS_MERGE' { | ||
| publishDir = [ enabled: false ] | ||
| publishDir = [ |
| } | ||
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| withName: 'SEQKIT_SPLIT2' { | ||
| ext.args = { "--by-size ${params.split_fastq}" } | ||
| publishDir = [ enabled: false ] | ||
| publishDir = [ |
| pattern: "*{metrics}" | ||
| ] | ||
| } | ||
| withName: 'GATK4_MARKDUPLICATES' { | ||
| ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT' | ||
| ext.suffix = '.md' | ||
| publishDir = [ | ||
| path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" }, | ||
| enabled: false | ||
| enabled: false, |
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see above, and the path could actually also be removed
| @@ -268,12 +268,12 @@ workflow SAREK { | |||
| ch_versions = ch_versions.mix(GATK4_MAPPING.out.versions) | |||
| } | |||
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| if (params.step == 'preparerecalibration') { | |||
| if (params.step == 'prepare_recalibration') { | |||
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Suggested change
| if (params.step == 'prepare_recalibration') { | |
| if (params.step == 'preparerecalibration') { |
workflows/sarek.nf
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| case 'recalibrate': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates.csv", checkIfExists: true); break | ||
| case 'variantcalling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break | ||
| case 'variant_calling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break |
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Suggested change
| case 'variant_calling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break | |
| case 'variantcalling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break |
workflows/sarek.nf
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| @@ -48,9 +48,9 @@ else { | |||
| log.warn "No samplesheet specified, attempting to restart from csv files present in ${params.outdir}" | |||
| switch (params.step) { | |||
| case 'mapping': exit 1, "Can't start with step $params.step without samplesheet" | |||
| case 'preparerecalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break | |||
| case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break | |||
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Suggested change
| case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break | |
| case 'preparerecalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break |
subworkflows/local/prepare_genome.nf
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| @@ -83,7 +83,7 @@ workflow PREPARE_GENOME { | |||
| } | |||
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| ch_known_indels_tbi = Channel.empty() | |||
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step)) { | |||
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'prepare_recalibration' in step)) { | |||
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Suggested change
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'prepare_recalibration' in step)) { | |
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step)) { |
subworkflows/local/prepare_genome.nf
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| @@ -69,7 +69,7 @@ workflow PREPARE_GENOME { | |||
| } | |||
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| ch_dbsnp_tbi = Channel.empty() | |||
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { | |||
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'prepare_recalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { | |||
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Suggested change
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'prepare_recalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { | |
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { |
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Before we can merge for sure, need to get the CI tests back to pass as well as the linting for sure 🙈 |
| @@ -1,6 +1,5 @@ | |||
| params { | |||
| outdir = "output/" | |||
| publish_dir_mode = "copy" | |||
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I think this might need to stay in for the CI tests to pass
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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You can check #468 for some updates, but we're probably going to get another PR whenever the tools release is happening (which I guess should be soon now) |
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maxulysse
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Feb 14, 2022
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| // Check input has been provided | ||
| if (!params.input) { | ||
| log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" | ||
| System.exit(1) | ||
| } |
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we need to have some work around for utilizing the automatic restart. This check totally negates the checks at workflows/sarek.nf lines 46 - 56
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hm ok I would say we need to fix sarek not the template then, what do you think?
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I think it's quite a useful feature to be able to restart the analysis. There is already a warning, and if the step isn't there it throws an error. You need to designate a step, which essentially is a shortcut for editing the config file. just set step = variant_calling instead of input = 'Path/To/Dir/preprocessing/csv/recalibrated.csv'
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right, I definitly think we should keep it, just make it work properly without messing with the template :)
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or otherwise we should raise the issue in tools and see i the template needs changing
maxulysse
reviewed
Feb 14, 2022
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| <<<<<<< HEAD | ||
| ======= | ||
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| >>>>>>> f1bcc423664ba9bcec1cd227225555971ef87a63 |
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Suggested change
| <<<<<<< HEAD | |
| ======= | |
| >>>>>>> f1bcc423664ba9bcec1cd227225555971ef87a63 |
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Still some comments not addressed, but looking better and better, I like the update on concat_vcf |
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This whole PR is still not right or up to date. But There is good conversation here. |
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PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).This PR seeks to fix 2 problems.
path,mode,pattern, andenabledkeywords. This should now address [BUG] modules.config: publishDirmode: 'copy' #471 and match the module stle