modules config update - preprocessing refactor #485
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| @@ -89,7 +89,7 @@ chr_dir = params.chr_dir ? Channel.fromPath(params.chr_dir). | |||
| chr_length = params.chr_length ? Channel.fromPath(params.chr_length).collect() : [] | |||
| dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.empty() | |||
| fasta = params.fasta ? Channel.fromPath(params.fasta).collect() : [] | |||
| germline_resource = params.germline_resource ? Channel.fromPath(params.germline_resource).collect() : [] | |||
| germline_resource = params.germline_resource ? Channel.fromPath(params.germline_resource).collect() : Channel.empty() | |||
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What is the difference again using [] and Channel.empty() ?
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not sure, but it wasn't working
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When creating a process input set, using Channel.empty() won't trigger the process to run, but if you give it [], the process runs with [] as the value for the corresponding parameter.
That's why channel.ifEmpty([]) is used so much for MULTIQC.
… + skip_markduplicates + skip_bqsr) into skip_tools
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
maxulysse
changed the title
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Stopping the refactoring here not to have a PR so huge it's a black hole that will swallow all the code reviewers |
OK, I'll figure out the rest of the CI and then call it a day |
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
| umi { | ||
| params.input = "${baseDir}/tests/csv/3.0/fastq_umi.csv" | ||
| params.umi_read_structure = '7M1S+T' | ||
| } | ||
| use_gatk_spark { | ||
| params.use_gatk_spark = 'baserecalibrator,markduplicates' | ||
| } | ||
| } | ||
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| //This is apparently useless as it won't overwrite things in the modules.config | ||
| process { |
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Think we can delete this now, no?
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Why not, we still want to test this no?
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it doesn't get overwritten but will need to be moved to the modules.config and activated somehow on test
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Only gatkspark test falling (on top on the previously variant calling too), but can't manage to make it work on my computer, and figure the current dev is actually not running gatk spark... |
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params.publish_dir_mode--skip_qc,--skip_markduplicatesand--skip_bqsrinto--skip_toolsext.whenfor modules in all current subworkflowsannotate.nfbam2fastq.nfgermline_variant_calling.nfmapping_csv.nfmarkduplicates_csv.nfpair_copy_number_calling.nfpair_variant_calling.nfprepare_genome.nfprepare_intervals.nfprepare_recalibration_csv.nfrecalibrate_csv.nfsplit_fastq.nftumor_variant_calling.nffastqc_trimgalore.nfmarkduplicates.nfprepare_recalibration.nfrecalibrate.nfannotation_ensemblvep/main.nfannotation_snpeff/main.nffgbio_create_umi_consensus/main.nfgatk4_mapping/main.nfgatk_tumor_normal_somatic_variant_calling/main.nfgatk_tumor_only_somatic_variant_calling/main.nfjoint_germline_variant_calling/main.nf