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clipper_ALS.wdl
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clipper_ALS.wdl
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version 1.0
workflow Call_Peaks {
input {
Array[File] samples
}
scatter (sample in samples) {
call Sort_Index_Bam {
input:
sample = sample
}
call Clipper {
input:
call_peak_bam = Sort_Index_Bam.sorted_indexed_bam,
call_peak_bai = Sort_Index_Bam.sorted_indexed_bai
}
}
}
task Sort_Index_Bam {
input {
File sample
}
String prefix = basename(sample,'_hg19.Aligned.out.bam')
command <<<
source /groups/cgsd/alexandre/miniconda3/etc/profile.d/conda.sh
conda activate eprint
samtools sort -O bam -m 2G -@ 20 -o ~{prefix}.bam ~{sample}
samtools index -b ~{prefix}.bam
>>>
runtime {
cpu: 20
memory: "40 GB"
}
output {
File sorted_indexed_bam = "~{prefix}.bam"
File sorted_indexed_bai = "~{prefix}.bam.bai"
}
}
task Clipper {
input {
File call_peak_bam
File call_peak_bai
}
String bed_peak_intervals = basename(call_peak_bam,'.bam') + '.bed'
command <<<
clipper \
--species hg19 \
--processors=16 \
--plot \
-v \
-q \
--bam ~{call_peak_bam} \
--outfile ~{bed_peak_intervals}
>>>
runtime {
cpu: 16
memory: "60 GB"
docker: "brianyee/clipper@sha256:094ede2a0ee7a6f2c2e07f436a8b63486dc4a072dbccad136b7a450363ab1876"
}
}