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SusiJoSusiJo
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Added output files to ASCAT (#1820)
* 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
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‎modules/ascat/main.nf‎

Lines changed: 27 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -17,12 +17,14 @@ process ASCAT {
1717
path(rt_file) // optional
1818

1919
output:
20-
tuple val(meta), path("*png"), emit: png
20+
tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs
21+
tuple val(meta), path("*BAF.txt"), emit: bafs
2122
tuple val(meta), path("*cnvs.txt"), emit: cnvs
23+
tuple val(meta), path("*LogR.txt"), emit: logrs
2224
tuple val(meta), path("*metrics.txt"), emit: metrics
25+
tuple val(meta), path("*png"), emit: png
2326
tuple val(meta), path("*purityploidy.txt"), emit: purityploidy
2427
tuple val(meta), path("*segments.txt"), emit: segments
25-
tuple val(meta), path("*alleleFrequencies_chr*.txt"), emit: allelefreqs
2628
path "versions.yml", emit: versions
2729

2830
when:
@@ -64,8 +66,8 @@ process ASCAT {
6466
ascat.prepareHTS(
6567
tumourseqfile = "$input_tumor",
6668
normalseqfile = "$input_normal",
67-
tumourname = "Tumour",
68-
normalname = "Normal",
69+
tumourname = paste0("$prefix", ".tumour"),
70+
normalname = paste0("$prefix", ".normal"),
6971
allelecounter_exe = "alleleCounter",
7072
alleles.prefix = allele_prefix,
7173
loci.prefix = loci_prefix,
@@ -85,16 +87,16 @@ process ASCAT {
8587
8688
#Load the data
8789
ascat.bc = ascat.loadData(
88-
Tumor_LogR_file = "Tumour_tumourLogR.txt",
89-
Tumor_BAF_file = "Tumour_normalBAF.txt",
90-
Germline_LogR_file = "Tumour_normalLogR.txt",
91-
Germline_BAF_file = "Tumour_normalBAF.txt",
90+
Tumor_LogR_file = paste0("$prefix", ".tumour_tumourLogR.txt"),
91+
Tumor_BAF_file = paste0("$prefix", ".tumour_tumourBAF.txt"),
92+
Germline_LogR_file = paste0("$prefix", ".tumour_normalLogR.txt"),
93+
Germline_BAF_file = paste0("$prefix", ".tumour_normalBAF.txt"),
9294
genomeVersion = "$genomeVersion",
9395
gender = "$gender"
9496
)
9597
9698
#Plot the raw data
97-
ascat.plotRawData(ascat.bc, img.prefix = "Before_correction_")
99+
ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".before_correction."))
98100
99101
# optional LogRCorrection
100102
if("$gc_input" != "NULL") {
@@ -104,12 +106,12 @@ process ASCAT {
104106
rt_input = paste0(normalizePath("$rt_input"), "/", "$rt_input", ".txt")
105107
ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = rt_input)
106108
#Plot raw data after correction
107-
ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_")
109+
ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc_rt."))
108110
}
109111
else {
110112
ascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = gc_input, replictimingfile = $rt_input)
111113
#Plot raw data after correction
112-
ascat.plotRawData(ascat.bc, img.prefix = "After_correction_GC_RT_")
114+
ascat.plotRawData(ascat.bc, img.prefix = paste0("$prefix", ".after_correction_gc."))
113115
}
114116
}
115117
@@ -165,26 +167,27 @@ process ASCAT {
165167
166168
"""
167169

168-
169170
stub:
170171
def prefix = task.ext.prefix ?: "${meta.id}"
171172
"""
173+
echo stub > ${prefix}.after_correction.gc_rt.test.tumour.germline.png
174+
echo stub > ${prefix}.after_correction.gc_rt.test.tumour.tumour.png
175+
echo stub > ${prefix}.before_correction.test.tumour.germline.png
176+
echo stub > ${prefix}.before_correction.test.tumour.tumour.png
172177
echo stub > ${prefix}.cnvs.txt
173178
echo stub > ${prefix}.metrics.txt
179+
echo stub > ${prefix}.normal_alleleFrequencies_chr21.txt
180+
echo stub > ${prefix}.normal_alleleFrequencies_chr22.txt
174181
echo stub > ${prefix}.purityploidy.txt
175182
echo stub > ${prefix}.segments.txt
176-
echo stub > Tumour.ASCATprofile.png
177-
echo stub > Tumour.ASPCF.png
178-
echo stub > Before_correction_Tumour.germline.png
179-
echo stub > After_correction_GC_Tumour.germline.png
180-
echo stub > Tumour.rawprofile.png
181-
echo stub > Tumour.sunrise.png
182-
echo stub > Before_correction_Tumour.tumour.png
183-
echo stub > After_correction_GC_Tumour.tumour.png
184-
echo stub > Tumour_alleleFrequencies_chr21.txt
185-
echo stub > Tumour_alleleFrequencies_chr22.txt
186-
echo stub > Normal_alleleFrequencies_chr21.txt
187-
echo stub > Normal_alleleFrequencies_chr22.txt
183+
echo stub > ${prefix}.tumour.ASPCF.png
184+
echo stub > ${prefix}.tumour.sunrise.png
185+
echo stub > ${prefix}.tumour_alleleFrequencies_chr21.txt
186+
echo stub > ${prefix}.tumour_alleleFrequencies_chr22.txt
187+
echo stub > ${prefix}.tumour_normalBAF.txt
188+
echo stub > ${prefix}.tumour_normalLogR.txt
189+
echo stub > ${prefix}.tumour_tumourBAF.txt
190+
echo stub > ${prefix}.tumour_tumourLogR.txt
188191
189192
echo "${task.process}:" > versions.yml
190193
echo ' alleleCounter: 4.3.0' >> versions.yml

‎tests/modules/ascat/test.yml‎

Lines changed: 15 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -3,17 +3,21 @@
33
tags:
44
- ascat
55
files:
6-
- path: output/ascat/After_correction_GC_Tumour.germline.png
7-
- path: output/ascat/After_correction_GC_Tumour.tumour.png
8-
- path: output/ascat/Before_correction_Tumour.germline.png
9-
- path: output/ascat/Before_correction_Tumour.tumour.png
10-
- path: output/ascat/Normal_alleleFrequencies_chr21.txt
11-
- path: output/ascat/Normal_alleleFrequencies_chr22.txt
6+
- path: output/ascat/test.after_correction.gc_rt.test.tumour.germline.png
7+
- path: output/ascat/test.after_correction.gc_rt.test.tumour.tumour.png
8+
- path: output/ascat/test.before_correction.test.tumour.germline.png
9+
- path: output/ascat/test.before_correction.test.tumour.tumour.png
1210
- path: output/ascat/test.cnvs.txt
11+
- path: output/ascat/test.metrics.txt
12+
- path: output/ascat/test.normal_alleleFrequencies_chr21.txt
13+
- path: output/ascat/test.normal_alleleFrequencies_chr22.txt
1314
- path: output/ascat/test.purityploidy.txt
1415
- path: output/ascat/test.segments.txt
15-
- path: output/ascat/Tumour_alleleFrequencies_chr21.txt
16-
- path: output/ascat/Tumour_alleleFrequencies_chr22.txt
17-
- path: output/ascat/Tumour.ASCATprofile.png
18-
- path: output/ascat/Tumour.rawprofile.png
19-
- path: output/ascat/Tumour.sunrise.png
16+
- path: output/ascat/test.tumour.ASPCF.png
17+
- path: output/ascat/test.tumour.sunrise.png
18+
- path: output/ascat/test.tumour_alleleFrequencies_chr21.txt
19+
- path: output/ascat/test.tumour_alleleFrequencies_chr22.txt
20+
- path: output/ascat/test.tumour_normalBAF.txt
21+
- path: output/ascat/test.tumour_normalLogR.txt
22+
- path: output/ascat/test.tumour_tumourBAF.txt
23+
- path: output/ascat/test.tumour_tumourLogR.txt

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