Long due nextflowmodules update#76
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ffmmulder wants to merge 10 commits intoUMCUGenetics:developfrom
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Release/v0.7.1
Release/v0.7.2
rernst
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Aug 22, 2023
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Nice work @ffmmulder
Some more general comments:
- Double check all
valinput/outputs. - Remove old sge configs
- Check code style, especially for long lines. Also try not to combine short and long arguments in one process, for example
-ivs--input. - Double check choice between
tuple(input1, input2)input and using multiple input channels. Did you make a choice on purpose?
input 1
input 2
BCFtools/1.17/MergeVCF.nf
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| shell = ['/bin/bash', '-euo', 'pipefail'] | ||
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| input: | ||
| tuple sample_id, file(bcf_file) |
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Make sure to add val: tuple(val(sample_id), file(bcf_file)).
BCFtools/1.17/View.nf
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| input: | ||
| tuple sample_id, file(bcf_file) |
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If you add an 'output extension' input/parameter you could in theory also use the same function to convert vcf to bcf.
| shell = ['/bin/bash', '-euo', 'pipefail'] | ||
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| input: | ||
| tuple(val(sample_id), val(rg_id), path(fastq)) |
| tag {"BWA_MEM2 BWASW ${sample_id} - ${rg_id}"} | ||
| label 'BWA_MEM2_2_2_1' | ||
| label 'BWA_MEM2_2_2_1_BWASW' | ||
| container = 'blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1' |
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Why do you need an container with samtools? Maybe just use bwa biocontainer?
| tag {"BWA_MEM2 Index $fasta"} | ||
| label 'BWA_MEM2_2_2_1' | ||
| label 'BWA_MEM2_2_2_1_Index' | ||
| container = 'library://blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1' |
GATK/4.3.0.0/GenotypeGVCFs.nf
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| tuple(val(run_id), val(interval), path(gvcf), path(gvcftbi), path(interval_file)) | ||
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| output: | ||
| tuple(val(run_id), val(interval), path("${run_id}.${interval}.${ext_vcf}"),path("${run_id}.${interval}.${ext_index}"),path(interval_file), emit : genotyped_vcfs) |
GATK/4.3.0.0/HaplotypeCaller.nf
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| tuple(val(sample_id), path(bam), path(bai), path(interval_file)) | ||
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| output: | ||
| tuple(val(sample_id), val(int_tag) ,path("${sample_id}.${int_tag}.${ext_vcf}"), path("${sample_id}.${int_tag}.${ext_index}"), path(interval_file), emit: htcaller_vcfs) |
| tuple(val(sample_id), path(bam_file), path(bai_file)) | ||
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| output: | ||
| tuple (val(sample_id), val(sample_id), path("${sample_id}.RG.bam"), path("${sample_id}.RG.bai"), emit: readgroup_bams) |
| tuple(val(sample_id), path(bam_file), path(bai_file)) | ||
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| output: | ||
| tuple(val(sample_id), val(sample_id), path("${sample_id}.RG.bam"), path("${sample_id}.RG.bai"), emit: readgroup_bams) |
Sambamba/0.8.2/MergeBams.nf
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| tag {"Sambamba MergeBams ${sample_id}"} | ||
| label 'Sambamba_0_8_2' | ||
| label 'Sambamba_0_8_2_MergeBams' | ||
| clusterOptions = workflow.profile == "sge" ? "-l h_vmem=${params.mem}" : "" |
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@ffmmulder What is the status of this PR? |
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Added some new tools/modules (such as AGAT, Deeplexicon,edgeR,DESeq2)
Updated module versions for all tools (to be used in v2 of NF-IAP/RNAseq pipelines)
Updated GATK tmpdir usage where not updated yet
Fixed/improved formatting where not updated yet
Other small (bug)fixes