Officially publish FASTA to new artifacts_root [#EO15]

CLIMB-COVID · Jan 25, 2022 · c1cb945 · c1cb945
1 parent 7983b85
commit c1cb945
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/elan.nf b/elan.nf
@@ -268,7 +268,6 @@ process rehead_fasta {
     tuple adm0, adm1, cor_date, seq_date, sourcesite, seqsite, tiles, platform, pipeuuid, username, dir, run_name, coguk_id, file(fasta), file(bam), file(depth) from swell_manifest_ch
 
     output:
-    publishDir path : "${params.publish}/staging/fasta/", pattern: "${coguk_id}.${run_name}.climb.fasta", mode: "copy", overwrite: true
     publishDir path : "${params.artifacts_root}/fasta/${params.datestamp}", pattern: "${coguk_id}.${run_name}.climb.fasta", mode: "copy", overwrite: true
     tuple sourcesite, seqsite, tiles, platform, pipeuuid, username, dir, run_name, coguk_id, file("${coguk_id}.${run_name}.climb.fasta"), file(bam), file(depth) into swell_ready_manifest_ch
 
@@ -357,7 +356,7 @@ process ocarina_ls {
     file "${coguk_id}.${run_name}.ocarina" into ocarina_report_ch
 
     """
-    echo "${coguk_id}\t${run_name}\t${username}\t${pipeuuid}\t${params.publish}/staging/\tfasta/${fasta}\t${params.artifacts_root}/bam/${params.datestamp}/${bam}\tqc/${qc}\t${sourcesite}\t${seqsite}\t${platform}" > ${coguk_id}.${run_name}.ocarina
+    echo "${coguk_id}\t${run_name}\t${username}\t${pipeuuid}\t${params.publish}/staging/\t${params.artifacts_root}/fasta/${params.datestamp}/${fasta}\t${params.artifacts_root}/bam/${params.datestamp}/${bam}\tqc/${qc}\t${sourcesite}\t${seqsite}\t${platform}" > ${coguk_id}.${run_name}.ocarina
     """
 }
 

diff --git a/ocarina.nf b/ocarina.nf
@@ -5,7 +5,7 @@
 Channel
     .fromPath(params.manifest)
     .splitCsv(header:['coguk_id', 'run_name', 'username', 'pipeuuid', 'dir', 'fasta', 'bam', 'qc', 'sourcesite', 'seqsite', 'platform'], sep:'\t')
-    .map { row-> tuple(row.coguk_id, row.run_name, row.username, row.pipeuuid, [row.dir, row.fasta].join('/'), row.bam, [row.dir, row.qc].join('/'), row.sourcesite, row.seqsite, row.platform) }
+    .map { row-> tuple(row.coguk_id, row.run_name, row.username, row.pipeuuid, row.fasta, row.bam, [row.dir, row.qc].join('/'), row.sourcesite, row.seqsite, row.platform) }
     .set { manifest_ch }
 
 process play_ocarina {