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add new fusion processes #3

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Aug 5, 2021
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23 changes: 12 additions & 11 deletions STARFusion/1.9.1/STARFusion.nf
Original file line number Diff line number Diff line change
@@ -1,24 +1,25 @@
process STAR_Fusion {
tag {"STAR_Fusion_${sample_id}"}
publishDir "${outdir}/STAR_Fusion", mode: 'copy'
shell = ['/bin/bash', '-euo', 'pipefail']
label 'process_medium'
process starFusion {

tag { "STAR_Fusion - ${sample_id}" }
publishDir "${outdir}/${sampleProject}/STAR_fusion", mode: 'copy'
label 'process_starfusion'

input:
tuple val(sample_id), file(read1), file(read2)
path genome_lib
tuple val(sample_id), file(reads)
path genome_lib

output:
tuple val(sample_id), val(outdir)
file("${sample_id}_star-fusion.tsv"),
file("${sample_id}_star-fusion.abridged.tsv")
file("${sample_id}_star-fusion.tsv"),
file("${sample_id}_star-fusion.abridged.tsv")

script:
"""
STAR-Fusion \
--genome_lib_dir ${genome_lib} \
--left_fq ${read1} \
--right_fq ${read2} \
--left_fq ${reads[0]} \
--right_fq ${reads[1]} \
--CPU ${task.cpus} \
--FusionInspector inspect \
--examine_coding_effect \
--denovo_reconstruct \
Expand Down
81 changes: 47 additions & 34 deletions arriba/2.1.0/Arriba.nf
Original file line number Diff line number Diff line change
@@ -1,47 +1,60 @@
process Arriba {
tag {"Arriba ${sample_id}"}
publishDir "${outdir}/Arriba", mode: 'copy'
shell = ['/bin/bash', '-euo', 'pipefail']
process arriba {

tag { "Arriba - ${sample_id}" }
publishDir "${outdir}/${sampleProject}/Arriba", mode: 'copy'
label 'process_arriba'

input:
tuple val(sample_id), file(reads)
path star_idx
path blacklist
path assembly
path annotation
val outdir
val opt_args
tuple val(sample_id), file(reads)
path star_idx
path blacklist
path assembly
path annotation
path known
path pdomains
val outdir
val opt_args

output:
tuple val(sample_id),
file("${sample_id}.arriba.fusions.tsv"),
file("${sample_id}.arriba.fusions.discarded.tsv")
file("${sample_id}.arriba.fusions.tsv"),
file("${sample_id}.arriba.fusions.discarded.tsv")

script:
"""
${opt_args}
--genomeLoad NoSharedMemory \
--outStd BAM_SortedByCoordinate \
--outSAMunmapped Within \
--outBAMcompression 0 \
--outFilterMultimapNmax 50 \
--peOverlapNbasesMin 10 \
--alignSplicedMateMapLminOverLmate 0.5 \
--alignSJstitchMismatchNmax 5 -1 5 5 \
--chimJunctionOverhangMin 10 \
--chimScoreDropMax 30 \
--chimScoreJunctionNonGTAG 0 \
--chimScoreSeparation 1 \
--chimSegmentReadGapMax 3 \
--chimMultimapNmax 50 |


arriba -b ${blacklist}.tsv.gz \
-x /dev/stdin \
STAR \
--runThreadN 8 \
--genomeDir ${star_idx} \
--genomeLoad NoSharedMemory \
--readFilesIn ${reads} \
--runThreadN ${task.cpus} \
--readFilesCommand zcat \
--outStd BAM_Unsorted \
--outSAMtype BAM Unsorted \
--outSAMunmapped Within \
--outBAMcompression 0 \
--outFilterMultimapNmax 50 \
--peOverlapNbasesMin 10 \
--alignSplicedMateMapLminOverLmate 0.5 \
--alignSJstitchMismatchNmax 5 -1 5 5 \
--chimSegmentMin 10 \
--chimOutType WithinBAM HardClip \
--chimJunctionOverhangMin 10 \
--chimScoreDropMax 30 \
--chimScoreJunctionNonGTAG 0 \
--chimScoreSeparation 1 \
--chimSegmentReadGapMax 3 \
--chimMultimapNmax 50 |
arriba \
-x /dev/stdin \
-o ${sample_id}.arriba.fusions.tsv \
-O ${sample_id}.arriba.fusions.discarded.tsv \
-a ${assembly}.fa \
-g ${annotation}.gtf \
-a ${annotation}.gtf \
-g ${annotation}.gtf \
-b ${blacklist}.tsv.gz \
-k ${known}.tsv.gz \
-t ${known}.tsv.gz \
-p ${pdomains}.gff3
"""
}