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Use publishDir to save final output files instead of manual copyTo #35

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merged 2 commits into from
Apr 26, 2021
Merged

Use publishDir to save final output files instead of manual copyTo #35

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affcf2d
Refactor to use publishDir to save final output files instead of manu…
ewels Apr 26, 2021
d73aeb2
Use closure for decoy publishDir
ewels Apr 26, 2021
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21 changes: 15 additions & 6 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -731,6 +731,12 @@ merged_databases = merged_databases.mix(cBioportal_proteindb)
*/
process merge_proteindbs {

publishDir "${params.outdir}/", mode: params.publish_dir_mode,
// Final step if not cleaning or creating a decoy database - save output to params.final_database_protein
saveAs: { filename ->
params.clean_database || params.decoy ? null : params.final_database_protein
}

input:
file("proteindb*") from merged_databases.collect()

Expand All @@ -748,6 +754,12 @@ process merge_proteindbs {
*/
process clean_protein_database {

publishDir "${params.outdir}/", mode: params.publish_dir_mode,
// Final step if not creating a decoy database - save output to params.final_database_protein
saveAs: { filename ->
params.decoy ? null : params.final_database_protein
}

when:
params.clean_database

Expand Down Expand Up @@ -782,6 +794,9 @@ to_protein_decoy_ch = params.clean_database ? clean_database_sh : to_clean_ch
*/
process decoy {

publishDir "${params.outdir}/", mode: params.publish_dir_mode,
saveAs: { filename -> params.final_database_protein }

when:
params.decoy

Expand All @@ -804,12 +819,6 @@ process decoy {
"""
}

result_database_ch = params.decoy ? fasta_decoy_db_ch: to_protein_decoy_ch

/** Write the final results to S3 bucket**/

result_database_ch.subscribe { results -> results.copyTo("${params.outdir}/${params.final_database_protein}")}


/*
* Output Description HTML
Expand Down