Refactor useq by sawibo · Pull Request #33 · UMCUGenetics/NextflowModules

sawibo · 2020-05-21T07:52:18Z

Made all the necessary refactoring changes. Tested in both the NF-IAP and IDT_SingleUMI_Pipeline development workflows.

tilschaef · 2020-05-22T11:03:45Z

BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf

+    shell = ['/bin/bash', '-euo', 'pipefail']
    input:
-    tuple sample_id, rg_id, file(fastq: "*")
+    tuple (sample_id, rg_id, path(fastq))


indentations

tilschaef · 2020-05-22T11:04:21Z

BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf


    output:
-    tuple sample_id, rg_id, file("${rg_id}_sorted.bam"),file("${rg_id}_sorted.bai")
+    tuple (sample_id, rg_id, path("${rg_id}_sorted.bam"),path("${rg_id}_sorted.bai"), emit: mapped_bams)


indentations

tilschaef · 2020-05-22T11:04:50Z

FastQC/0.11.5/FastQC.nf


    input:
-    tuple sample_id, rg_id, file(fastq: "*")
+    tuple (sample_id, rg_id, path(fastq) )


indentations

tilschaef · 2020-05-22T11:06:17Z

GATK/4.1.3.0/BaseRecalibration.nf

-
+    shell = ['/bin/bash', '-euo', 'pipefail']
    input:
-      tuple sample_id, file(bam), file(bai),file(recal_table), file(interval_file)


-2 tabs indentation

tilschaef · 2020-05-22T11:06:53Z

GATK/4.1.3.0/BaseRecalibrationTable.nf

+      tuple (sample_id, path("${sample_id}.${int_tag}.recal.table"), emit: recalibration_tables)

    script:
    known = params.genome_known_sites ? '--known-sites ' + params.genome_known_sites.join(' --known-sites ') : ''


-indentations

tilschaef · 2020-05-22T11:07:55Z

GATK/4.1.3.0/CombineGVCFs.nf

+      tuple (run_id, interval, path(gvcf_chunks), path(gvcf_chunk_idxs), path(interval_file))
    output:
-      tuple run_id, interval, file("${run_id}.${interval}.g.vcf"), file("${run_id}.${interval}.g.vcf.idx"),file(interval_file)
+      tuple (run_id, interval, path("${run_id}.${interval}.g.vcf"), path("${run_id}.${interval}.g.vcf.idx"),path(interval_file), emit: combined_gvcfs)


-spatie na comma

tilschaef · 2020-05-22T11:08:44Z

GATK/4.1.3.0/HaplotypeCaller.nf

+      tuple (sample_id, int_tag ,path("${sample_id}.${int_tag}${ext}"), path("${sample_id}.${int_tag}${ext}.idx"), path(interval_file), emit: htcaller_vcfs)

    script:
    int_tag = interval_file.toRealPath().toString().split("/")[-2]


indent script section

tilschaef · 2020-05-22T11:09:48Z

GATK/4.1.3.0/SamToFastq.nf

-    // publishDir params.out_dir, mode: 'copy'
    input:
-      tuple sample_id, flowcell, machine, run_nr,file(bam)
+      tuple (sample_id, flowcell, machine, run_nr,path(bam))


spatie na comma

tilschaef · 2020-05-22T11:11:16Z

GATK/4.1.3.0/VariantAnnotator.nf

+      tuple (run_id, path("${vcf.baseName}_${db_name}.vcf"), path("${vcf.baseName}_${db_name}.vcf.idx"), emit: annotated_vcfs)

    script:
    db_file = file(params.genome_variant_annotator_db).getBaseName()


indent script section

tilschaef · 2020-05-22T11:11:36Z

GATK/4.1.3.0/VariantFiltration.nf

+      tuple (run_id, interval, type, path("${run_id}.${interval}.${type}.filtered_variants.vcf"), path("${run_id}.${interval}.${type}.filtered_variants.vcf.idx"), emit: filtered_vcfs)

    script:
    if (type == 'SNP'){


indent script section

tilschaef · 2020-05-22T11:12:50Z

MultiQC/1.5/MultiQC.nf

-
+    shell = ['/bin/bash', '-euo', 'pipefail']
    input:
-


Add title argument

tilschaef · 2020-05-22T11:13:55Z

fgbio/1.1.0/CallMolecularConsensusReads.nf

    script:

    """
    java -Xmx${task.memory.toGiga()-4}g -jar /bin/fgbio-1.1.0.jar --tmp-dir \$PWD CallMolecularConsensusReads \


indent script section

tilschaef · 2020-05-22T11:14:19Z

fgbio/1.1.0/FilterConsensusReads.nf

@@ -17,6 +18,6 @@ process FilterConsensusReads {
    --input $bam \


indent script section

tilschaef · 2020-05-22T11:14:45Z

fgbio/1.1.0/SortBam.nf

    script:

    """
    java -Xmx${task.memory.toGiga()-4}g -jar /bin/fgbio-1.1.0.jar --tmp-dir \$PWD SortBam \


indent script section

tilschaef · 2020-05-22T11:15:11Z

python/CountUmiFamilies.nf

    shell = ['/bin/bash', '-euo', 'pipefail']

    input:
-    tuple sample_id, flowcell, machine, run_nr, file(bam)


indent section

tilschaef · 2020-05-22T11:15:44Z

snpEff/4.3t/SnpSiftAnnotate.nf

+      tuple (run_id, path("${vcf.baseName}_${db_name}.vcf"), path("${vcf.baseName}_${db_name}.vcf.idx"), emit: snpsift_annoted_vcfs)

    script:
    db_file = file(params.genome_snpsift_annotate_db).getBaseName()


indent script section

tilschaef · 2020-05-22T11:16:08Z

snpEff/4.3t/snpEffFilter.nf

    script:

    """
-    set -o pipefail


indent script section

tilschaef

Indent all sections by 4 spaces (input, output, script).
Check spaces after commas for output tuples.
Leave space between sections.

tilschaef

Check indentations. Sometimes they vary between 3 and 4. Looking good so far.

Sander Boymans and others added 7 commits May 12, 2020 10:57

Recoded MakeUmiBam, added support for R3 fastq

fcfbc33

Merge branch 'dev-useq' into refactor-useq

ba41959

named output, name changes & path instead of file

3a5b23f

2nd refactor of code

764b1fe

Refactoring bug fixes

bb703fd

Refactoring bug fix

6404ab6

Merge branch 'develop' into refactor-useq

b4a9c38

tilschaef reviewed May 22, 2020

View reviewed changes

MultiQC/1.5/MultiQC.nf

shell = ['/bin/bash', '-euo', 'pipefail']

input:

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Add title argument

tilschaef reviewed May 22, 2020

View reviewed changes

snpEff/4.3t/snpEffFilter.nf

script:

"""

set -o pipefail

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indent script section

tilschaef suggested changes May 22, 2020

View reviewed changes

sawibo added 5 commits May 22, 2020 13:52

Update Mapping.nf

4d77686

Update Index.nf

a5f7614

Update FastQC.nf

d79e62e

Update BaseRecalibration.nf

f1b437f

Update BaseRecalibrationTable.nf

3524ce7

sawibo added 27 commits May 22, 2020 14:04

Update FastQC.nf

905d189

Update BaseRecalibration.nf

5f79e7b

Update BaseRecalibrationTable.nf

98468dc

Update CollectMultipleMetrics.nf

1ea20fd

Update CollectWGSMetrics.nf

58711be

Update CombineGVCFs.nf

38f77ca

Update GatherBaseRecalibrationTables.nf

1068389

Update GenotypeGVCFs.nf

2cc49d0

Update HaplotypeCaller.nf

17d769e

Update MergeVCFs.nf

e563367

Update SamToFastq.nf

52fada6

Update SelectVariants.nf

67343cb

Update SplitIntervals.nf

17f74c9

Update VariantAnnotator.nf

8729b04

Update VariantFiltration.nf

d4890d4

Update MultiQC.nf

92d14c4

Update MarkDup.nf

0a801bc

Update MergeBams.nf

eb26302

Update MergeFastQs.nf

9fa3a24

Update CallMolecularConsensusReads.nf

7c8c1e6

Update FilterConsensusReads.nf

2af8c0a

Update SortBam.nf

c117028

Update CountUmiFamilies.nf

29455d7

Update MakeUmiBam.nf

67cb3b3

Update SnpSiftAnnotate.nf

4b1f414

Update SnpSiftDbnsfp.nf

0fefdcb

Update snpEffFilter.nf

6069df1

tilschaef approved these changes May 22, 2020

View reviewed changes

sawibo merged commit 6387e87 into develop May 25, 2020

rernst deleted the refactor-useq branch May 27, 2020 09:01

		@@ -17,6 +18,6 @@ process FilterConsensusReads {
		--input $bam \

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sawibo commented May 21, 2020

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tilschaef May 22, 2020 •

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