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Added output files to ASCAT #1820

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Merged
SusiJo merged 27 commits into from
Jun 28, 2022
Merged

Added output files to ASCAT #1820

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3d70fbd
add unzip alleles + loci
SusiJo Jun 15, 2022
9c10907
fix the partial absolute prefix path
SusiJo Jun 15, 2022
024edea
exchanged deprecated function + added metrics
SusiJo Jun 17, 2022
1921ed8
updated meta
SusiJo Jun 17, 2022
4839548
tested logRCorrection + cram input
SusiJo Jun 17, 2022
f8710c5
added BED for WES
SusiJo Jun 17, 2022
daeb89f
added outputs + alleleCounter version
SusiJo Jun 20, 2022
d42927c
test samtools chr operations, fixed cancerit conda
SusiJo Jun 20, 2022
39f10c6
ch formatting, fasta, bed input
SusiJo Jun 21, 2022
e837612
comment out local tests
SusiJo Jun 23, 2022
23de707
added metrics, bed, ref_fasta
SusiJo Jun 23, 2022
1b0f410
Merge branch 'nf-core:master' into ascat
SusiJo Jun 23, 2022
5d0ceb5
rm print statement
SusiJo Jun 23, 2022
55c8c88
added stub outputs
SusiJo Jun 23, 2022
514bad5
rm versions.yml
SusiJo Jun 23, 2022
d2a5142
fix linting
SusiJo Jun 23, 2022
fa64d36
rm fictitious md5sums for stub-run
SusiJo Jun 23, 2022
d205dbf
try fixing top-level of stub versions.yml
SusiJo Jun 23, 2022
3bdefdb
ordered inputs alphabetically, ref_fasta -> fasta
SusiJo Jun 23, 2022
0e67aee
rm R system command, adjust meta.yml
SusiJo Jun 23, 2022
29fde8f
prettier yml
SusiJo Jun 23, 2022
f3f297f
added outputs + prefix to outputs
SusiJo Jun 28, 2022
9d1d9ec
Merge remote-tracking branch 'origin/master' into ascat
SusiJo Jun 28, 2022
e41fc8e
added test-yml outputs
SusiJo Jun 28, 2022
8cafc77
Merge remote-tracking branch 'origin/master' into ascat
SusiJo Jun 28, 2022
fea00e1
change underscores to dots
SusiJo Jun 28, 2022
59a4e44
Merge remote-tracking branch 'origin/master' into ascat
SusiJo Jun 28, 2022
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51 changes: 27 additions & 24 deletions modules/ascat/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,12 +17,14 @@ process ASCAT {
path(rt_file) // optional

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("*LogR.txt"), emit: logrs
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("*segments.txt"), emit: segments
tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs
path "versions.yml", emit: versions

when:
Expand Down Expand Up @@ -64,8 +66,8 @@ process ASCAT {
ascat.prepareHTS(
tumourseqfile = "$input_tumor",
normalseqfile = "$input_normal",
tumourname = "Tumour",
normalname = "Normal",
tumourname = paste0("$prefix", ".tumour"),
normalname = paste0("$prefix", ".normal"),
allelecounter_exe = "alleleCounter",
alleles.prefix = allele_prefix,
loci.prefix = loci_prefix,
Expand All @@ -85,16 +87,16 @@ process ASCAT {

#Load the data
ascat.bc = ascat.loadData(
Tumor_LogR_file = "Tumour_tumourLogR.txt",
Tumor_BAF_file = "Tumour_normalBAF.txt",
Germline_LogR_file = "Tumour_normalLogR.txt",
Germline_BAF_file = "Tumour_normalBAF.txt",
Tumor_LogR_file = paste0("$prefix", ".tumour_tumourLogR.txt"),
Tumor_BAF_file = paste0("$prefix", ".tumour_tumourBAF.txt"),
Germline_LogR_file = paste0("$prefix", ".tumour_normalLogR.txt"),
Germline_BAF_file = paste0("$prefix", ".tumour_normalBAF.txt"),
genomeVersion = "$genomeVersion",
gender = "$gender"
)

#Plot the raw data
ascat.plotRawData(ascat.bc, img.prefix = "Before_correction_")
ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".before_correction."))

# optional LogRCorrection
if("$gc_input" != "NULL") {
Expand All @@ -104,12 +106,12 @@ process ASCAT {
rt_input = paste0(normalizePath("$rt_input"), "/", "$rt_input", ".txt")
ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = rt_input)
#Plot raw data after correction
ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_")
ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc_rt."))
}
else {
ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = $rt_input)
#Plot raw data after correction
ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_RT_")
ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc."))
}
}

Expand Down Expand Up @@ -165,26 +167,27 @@ process ASCAT {

"""


stub:
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}.metrics.txt
echo stub > ${prefix}.normal_alleleFrequencies_chr21.txt
echo stub > ${prefix}.normal_alleleFrequencies_chr22.txt
echo stub > ${prefix}.purityploidy.txt
echo stub > ${prefix}.segments.txt
echo stub > Tumour.ASCATprofile.png
echo stub > Tumour.ASPCF.png
echo stub > Before_correction_Tumour.germline.png
echo stub > After_correction_GC_Tumour.germline.png
echo stub > Tumour.rawprofile.png
echo stub > Tumour.sunrise.png
echo stub > Before_correction_Tumour.tumour.png
echo stub > After_correction_GC_Tumour.tumour.png
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 stub > ${prefix}.tumour.ASPCF.png
echo stub > ${prefix}.tumour.sunrise.png
echo stub > ${prefix}.tumour_alleleFrequencies_chr21.txt
echo stub > ${prefix}.tumour_alleleFrequencies_chr22.txt
echo stub > ${prefix}.tumour_normalBAF.txt
echo stub > ${prefix}.tumour_normalLogR.txt
echo stub > ${prefix}.tumour_tumourBAF.txt
echo stub > ${prefix}.tumour_tumourLogR.txt

echo "${task.process}:" > versions.yml
echo ' alleleCounter: 4.3.0' >> versions.yml
Expand Down
26 changes: 15 additions & 11 deletions tests/modules/ascat/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,17 +3,21 @@
tags:
- ascat
files:
- path: output/ascat/After_correction_GC_Tumour.germline.png
- path: output/ascat/After_correction_GC_Tumour.tumour.png
- path: output/ascat/Before_correction_Tumour.germline.png
- path: output/ascat/Before_correction_Tumour.tumour.png
- path: output/ascat/Normal_alleleFrequencies_chr21.txt
- path: output/ascat/Normal_alleleFrequencies_chr22.txt
- path: output/ascat/test.after_correction.gc_rt.test.tumour.germline.png
- path: output/ascat/test.after_correction.gc_rt.test.tumour.tumour.png
- path: output/ascat/test.before_correction.test.tumour.germline.png
- path: output/ascat/test.before_correction.test.tumour.tumour.png
- 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.segments.txt
- path: output/ascat/Tumour_alleleFrequencies_chr21.txt
- path: output/ascat/Tumour_alleleFrequencies_chr22.txt
- path: output/ascat/Tumour.ASCATprofile.png
- path: output/ascat/Tumour.rawprofile.png
- path: output/ascat/Tumour.sunrise.png
- path: output/ascat/test.tumour.ASPCF.png
- path: output/ascat/test.tumour.sunrise.png
- path: output/ascat/test.tumour_alleleFrequencies_chr21.txt
- path: output/ascat/test.tumour_alleleFrequencies_chr22.txt
- 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