kfukuta/wf-transcriptomes-v202
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Merge branch 'CW-4613-b' into 'dev'

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IGV absolute paths fix

Closes CW-4613

See merge request epi2melabs/workflows/wf-transcriptomes!184
This commit is contained in:
Sam Nicholls 2024-09-13 11:48:16 +00:00
commit beb094ea85
2 changed files with 5 additions and 6 deletions
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9
main.nf
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@ -779,7 +779,6 @@ workflow pipeline {
if (params.transcriptome_source != "precomputed" && params.igv){ if (params.transcriptome_source != "precomputed" && params.igv){
is_compressed = file("${params.ref_genome}").extension == "gz" is_compressed = file("${params.ref_genome}").extension == "gz"
String publish_ref = "igv_reference" String publish_ref = "igv_reference"
String current_dir = "${file('.').toUriString()}"
reference_genome = Channel.fromPath("${params.ref_genome}") reference_genome = Channel.fromPath("${params.ref_genome}")
igv_ref = reference_genome | flatten | map { it -> "${it.toUriString()}" } igv_ref = reference_genome | flatten | map { it -> "${it.toUriString()}" }
if (is_compressed){ if (is_compressed){
@ -797,7 +796,7 @@ workflow pipeline {
} else { } else {
gz_igv = gz_faidx(Channel.fromPath("${params.ref_genome}")) gz_igv = gz_faidx(Channel.fromPath("${params.ref_genome}"))
| flatten | flatten
| map { it -> "$current_dir/$params.out_dir/$publish_ref/${it.Name}" } | map { it -> "$publish_ref/${it.Name}" }
gz_igv | ifEmpty{ gz_igv | ifEmpty{
if (params.containsKey("igv") && params.igv){ if (params.containsKey("igv") && params.igv){
log.warn """\ log.warn """\
@ -819,7 +818,7 @@ workflow pipeline {
igv_index = ref_idx | flatten | map { it -> "${it.toUriString()}" } igv_index = ref_idx | flatten | map { it -> "${it.toUriString()}" }
} else { } else {
ref_idx = faidx(reference_genome) ref_idx = faidx(reference_genome)
igv_index = ref_idx | map { it -> "$current_dir/$params.out_dir/$publish_ref/${it.Name}" } igv_index = ref_idx | map { it -> "$publish_ref/${it.Name}" }
} }
// get list of file names // get list of file names
@ -829,8 +828,8 @@ workflow pipeline {
| toSortedList | toSortedList
| map { list -> list.collect{ | map { list -> list.collect{
[ [
"$current_dir/$params.out_dir/$publish_bams/${it}_reads_aln_sorted.bam", "$publish_bams/${it}_reads_aln_sorted.bam",
"$current_dir/$params.out_dir/$publish_bams/${it}_reads_aln_sorted.bam.bai" "$publish_bams/${it}_reads_aln_sorted.bam.bai"
] ]
} } } }
| concat ( igv_index) | concat ( igv_index)

2
subworkflows/differential_expression.nf
View File

@ -107,7 +107,7 @@ process plotResults {
""" """
plot_dtu_results.R plot_dtu_results.R
# output plots to common analysis output directory # output plots to common analysis output directory
mv dtu_plots.pdf de_analysis/dtu_plots.pdf cp dtu_plots.pdf de_analysis/dtu_plots.pdf
""" """
} }