diff --git a/src/nf_modules/deepTools/compute_matrix.nf b/src/nf_modules/deepTools/compute_matrix.nf index e9de41365b68c09018adb53809466589dc4bbcd9..d1d0ae07def09062c93f57dfac54b75734cfdb55 100644 --- a/src/nf_modules/deepTools/compute_matrix.nf +++ b/src/nf_modules/deepTools/compute_matrix.nf @@ -1,4 +1,4 @@ -params.bam = "$baseDir/data/bigwig/*.bw" +params.bw = "$baseDir/data/bigwig/*.bw" params.bed = "$baseDir/data/annot/*.bed" log.info "bigwig files : ${params.bw}" @@ -7,7 +7,6 @@ log.info "bed files : ${params.bed}" Channel .fromPath( params.bw ) .ifEmpty { error "Cannot find any bigwig files matching: ${params.bw}" } - .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]} .set { bw_files } Channel @@ -17,12 +16,12 @@ Channel .set { bed_files } process compute_matrix { - tag "$file_id" + tag "$bed_file_id" cpus 4 publishDir "results/mapping/region_matrix/", mode: 'copy' input: - set bw_file_id, file(bw) from bw_files.collect() + file bw from bw_files.collect() set bed_file_id, file(bed) from bed_files.collect() output: diff --git a/src/nf_modules/deepTools/tests.sh b/src/nf_modules/deepTools/tests.sh index 06057a81e896dde34b2261f8a48d187d4e6e11f0..f6950b96a5d5ed56ed1fac24e1fbd9125d0cf7df 100755 --- a/src/nf_modules/deepTools/tests.sh +++ b/src/nf_modules/deepTools/tests.sh @@ -1,6 +1,8 @@ #!/bin/sh -./nextflow src/nf_modules/deepTools/bam_to_bigwig.nf -c src/nf_modules/deepTools/bam_to_bigwig.config -profile docker --bam "data/tiny_dataset/map/tiny_v2.sort.bam" +cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_bis.sort.bam + +./nextflow src/nf_modules/deepTools/bam_to_bigwig.nf -c src/nf_modules/deepTools/bam_to_bigwig.config -profile docker --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" ./nextflow src/nf_modules/deepTools/compute_matrix.nf -c src/nf_modules/deepTools/compute_matrix.config -profile docker --bw "results/mapping/bigwig/*.bw" --bed "data/tiny_dataset/annot/tiny.bed"