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Co-authored-by: Friederike Hanssen <[email protected]>
asp8200 · Jul 13, 2023 · 6e3bb60 · 6e3bb60
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commit 6e3bb60
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diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -36,7 +36,7 @@
             },
             "status": {
                 "type": "integer",
-                "errorMessage": "Status can only be 0 or 1. Defaults to 0, if none is supplied.",
+                "errorMessage": "Status can only be 0 (normal) or 1 (tumor). Defaults to 0, if none is supplied.",
                 "meta": ["status"],
                 "default": 0,
                 "minimum": 0,

diff --git a/workflows/sarek.nf b/workflows/sarek.nf
@@ -94,11 +94,10 @@ ch_from_samplesheet
         def flowcell   = flowcellLaneFromFastq(fastq_1)
         // Don't use a random element for ID, it breaks resuming
         def read_group = "\"@RG\\tID:${flowcell}.${meta.sample}.${meta.lane}\\t${CN}PU:${meta.lane}\\tSM:${meta.patient}_${meta.sample}\\tLB:${meta.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\""
-        println "Number of lanes: $num_lanes"
 
         meta           = meta + [num_lanes: num_lanes.toInteger(), read_group: read_group.toString(), data_type: 'fastq', size: 1]
 
-        if (params.step == 'mapping') return [ meta - meta.subMap('lane'), [ fastq_1, fastq_2 ] ]
+        if (params.step == 'mapping') return [ meta, [ fastq_1, fastq_2 ] ]
         else {
             error("Samplesheet contains fastq files but step is `$params.step`. Please check your samplesheet or adjust the step parameter.\nhttps://nf-co.re/sarek/usage#input-samplesheet-configurations")
         }