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Added output files to ASCAT (#1820)

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* add unzip alleles + loci

* fix the partial absolute prefix path

* exchanged deprecated function + added metrics

* updated meta

* tested logRCorrection + cram input

* added BED for WES

* added outputs + alleleCounter version

* test samtools chr operations, fixed cancerit conda

* ch formatting, fasta, bed input

* comment out local tests

* added metrics, bed, ref_fasta

* rm print statement

* added stub outputs

* rm versions.yml

* fix linting

* rm fictitious md5sums for stub-run

* try fixing top-level of stub versions.yml

* ordered inputs alphabetically, ref_fasta -> fasta

* rm R system command, adjust meta.yml

* prettier yml

* added outputs + prefix to outputs

* added test-yml outputs

* change underscores to dots
This commit is contained in:
SusiJo 2022-06-28 14:45:57 +02:00 committed by GitHub
parent a9521de5ac
commit 98ffb09002
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2 changed files with 42 additions and 35 deletions
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51
modules/ascat/main.nf
View file

@ -17,12 +17,14 @@ process ASCAT {
path(rt_file) // optional path(rt_file) // optional
output: output:
tuple val(meta), path("*png"), emit: png tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs
tuple val(meta), path("*BAF.txt"), emit: bafs
tuple val(meta), path("*cnvs.txt"), emit: cnvs tuple val(meta), path("*cnvs.txt"), emit: cnvs
tuple val(meta), path("*LogR.txt"), emit: logrs
tuple val(meta), path("*metrics.txt"), emit: metrics tuple val(meta), path("*metrics.txt"), emit: metrics
tuple val(meta), path("*png"), emit: png
tuple val(meta), path("*purityploidy.txt"), emit: purityploidy tuple val(meta), path("*purityploidy.txt"), emit: purityploidy
tuple val(meta), path("*segments.txt"), emit: segments tuple val(meta), path("*segments.txt"), emit: segments
tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs
path "versions.yml", emit: versions path "versions.yml", emit: versions
when: when:
@ -64,8 +66,8 @@ process ASCAT {
ascat.prepareHTS( ascat.prepareHTS(
tumourseqfile = "$input_tumor", tumourseqfile = "$input_tumor",
normalseqfile = "$input_normal", normalseqfile = "$input_normal",
tumourname = "Tumour", tumourname = paste0("$prefix", ".tumour"),
normalname = "Normal", normalname = paste0("$prefix", ".normal"),
allelecounter_exe = "alleleCounter", allelecounter_exe = "alleleCounter",
alleles.prefix = allele_prefix, alleles.prefix = allele_prefix,
loci.prefix = loci_prefix, loci.prefix = loci_prefix,
@ -85,16 +87,16 @@ process ASCAT {
#Load the data #Load the data
ascat.bc = ascat.loadData( ascat.bc = ascat.loadData(
Tumor_LogR_file = "Tumour_tumourLogR.txt", Tumor_LogR_file = paste0("$prefix", ".tumour_tumourLogR.txt"),
Tumor_BAF_file = "Tumour_normalBAF.txt", Tumor_BAF_file = paste0("$prefix", ".tumour_tumourBAF.txt"),
Germline_LogR_file = "Tumour_normalLogR.txt", Germline_LogR_file = paste0("$prefix", ".tumour_normalLogR.txt"),
Germline_BAF_file = "Tumour_normalBAF.txt", Germline_BAF_file = paste0("$prefix", ".tumour_normalBAF.txt"),
genomeVersion = "$genomeVersion", genomeVersion = "$genomeVersion",
gender = "$gender" gender = "$gender"
) )
#Plot the raw data #Plot the raw data
ascat.plotRawData(ascat.bc, img.prefix = "Before_correction_") ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".before_correction."))
# optional LogRCorrection # optional LogRCorrection
if("$gc_input" != "NULL") { if("$gc_input" != "NULL") {
@ -104,12 +106,12 @@ process ASCAT {
rt_input = paste0(normalizePath("$rt_input"), "/", "$rt_input", ".txt") rt_input = paste0(normalizePath("$rt_input"), "/", "$rt_input", ".txt")
ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = rt_input) ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = rt_input)
#Plot raw data after correction #Plot raw data after correction
ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_") ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc_rt."))
} }
else { else {
ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = $rt_input) ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = $rt_input)
#Plot raw data after correction #Plot raw data after correction
ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_RT_") ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc."))
} }
} }
@ -165,26 +167,27 @@ process ASCAT {
""" """
stub: stub:
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
echo stub > ${prefix}.after_correction.gc_rt.test.tumour.germline.png
echo stub > ${prefix}.after_correction.gc_rt.test.tumour.tumour.png
echo stub > ${prefix}.before_correction.test.tumour.germline.png
echo stub > ${prefix}.before_correction.test.tumour.tumour.png
echo stub > ${prefix}.cnvs.txt echo stub > ${prefix}.cnvs.txt
echo stub > ${prefix}.metrics.txt echo stub > ${prefix}.metrics.txt
echo stub > ${prefix}.normal_alleleFrequencies_chr21.txt
echo stub > ${prefix}.normal_alleleFrequencies_chr22.txt
echo stub > ${prefix}.purityploidy.txt echo stub > ${prefix}.purityploidy.txt
echo stub > ${prefix}.segments.txt echo stub > ${prefix}.segments.txt
echo stub > Tumour.ASCATprofile.png echo stub > ${prefix}.tumour.ASPCF.png
echo stub > Tumour.ASPCF.png echo stub > ${prefix}.tumour.sunrise.png
echo stub > Before_correction_Tumour.germline.png echo stub > ${prefix}.tumour_alleleFrequencies_chr21.txt
echo stub > After_correction_GC_Tumour.germline.png echo stub > ${prefix}.tumour_alleleFrequencies_chr22.txt
echo stub > Tumour.rawprofile.png echo stub > ${prefix}.tumour_normalBAF.txt
echo stub > Tumour.sunrise.png echo stub > ${prefix}.tumour_normalLogR.txt
echo stub > Before_correction_Tumour.tumour.png echo stub > ${prefix}.tumour_tumourBAF.txt
echo stub > After_correction_GC_Tumour.tumour.png echo stub > ${prefix}.tumour_tumourLogR.txt
echo stub > Tumour_alleleFrequencies_chr21.txt
echo stub > Tumour_alleleFrequencies_chr22.txt
echo stub > Normal_alleleFrequencies_chr21.txt
echo stub > Normal_alleleFrequencies_chr22.txt
echo "${task.process}:" > versions.yml echo "${task.process}:" > versions.yml
echo ' alleleCounter: 4.3.0' >> versions.yml echo ' alleleCounter: 4.3.0' >> versions.yml

26
tests/modules/ascat/test.yml
View file

@ -3,17 +3,21 @@
tags: tags:
- ascat - ascat
files: files:
- path: output/ascat/After_correction_GC_Tumour.germline.png - path: output/ascat/test.after_correction.gc_rt.test.tumour.germline.png
- path: output/ascat/After_correction_GC_Tumour.tumour.png - path: output/ascat/test.after_correction.gc_rt.test.tumour.tumour.png
- path: output/ascat/Before_correction_Tumour.germline.png - path: output/ascat/test.before_correction.test.tumour.germline.png
- path: output/ascat/Before_correction_Tumour.tumour.png - path: output/ascat/test.before_correction.test.tumour.tumour.png
- path: output/ascat/Normal_alleleFrequencies_chr21.txt
- path: output/ascat/Normal_alleleFrequencies_chr22.txt
- path: output/ascat/test.cnvs.txt - path: output/ascat/test.cnvs.txt
- path: output/ascat/test.metrics.txt
- path: output/ascat/test.normal_alleleFrequencies_chr21.txt
- path: output/ascat/test.normal_alleleFrequencies_chr22.txt
- path: output/ascat/test.purityploidy.txt - path: output/ascat/test.purityploidy.txt
- path: output/ascat/test.segments.txt - path: output/ascat/test.segments.txt
- path: output/ascat/Tumour_alleleFrequencies_chr21.txt - path: output/ascat/test.tumour.ASPCF.png
- path: output/ascat/Tumour_alleleFrequencies_chr22.txt - path: output/ascat/test.tumour.sunrise.png
- path: output/ascat/Tumour.ASCATprofile.png - path: output/ascat/test.tumour_alleleFrequencies_chr21.txt
- path: output/ascat/Tumour.rawprofile.png - path: output/ascat/test.tumour_alleleFrequencies_chr22.txt
- path: output/ascat/Tumour.sunrise.png - path: output/ascat/test.tumour_normalBAF.txt
- path: output/ascat/test.tumour_normalLogR.txt
- path: output/ascat/test.tumour_tumourBAF.txt
- path: output/ascat/test.tumour_tumourLogR.txt