Merge branch 'temp-up' into 'dev'

Temp up

See merge request epi2melabs/workflows/wf-transcriptomes!147

lib/ingress.nf

@@ -149,13 +149,12 @@ def xam_ingress(Map arguments)
 
     def input = get_valid_inputs(margs, xam_extensions)
 
+    // check BAM headers to see if any samples are uBAM
     ch_result = input.dirs
     | map { meta, path -> [meta, get_target_files_in_dir(path, xam_extensions)] }
     | mix(input.files)
-
-    ch_is_unaligned = ch_result
     | checkBamHeaders
-    | map { meta, is_unaligned_env, mixed_headers_env ->
+    | map { meta, paths, is_unaligned_env, mixed_headers_env ->
         // convert the env. variables from strings ('0' or '1') into bools
         boolean is_unaligned = is_unaligned_env as int as boolean
         boolean mixed_headers = mixed_headers_env as int as boolean
@@ -163,14 +162,11 @@ def xam_ingress(Map arguments)
         if (mixed_headers) {
             error "Found mixed headers in (u)BAM files of sample '${meta.alias}'."
         }
-        [meta, is_unaligned]
+        // add `is_unaligned` to the metamap (note the use of `+` to create a copy of
+        // `meta` to avoid modifying every item in the channel;
+        // https://github.com/nextflow-io/nextflow/issues/2660)
+        [meta + [is_unaligned: is_unaligned], paths]
     }
-
-    ch_result = ch_result | join(ch_is_unaligned)
-    // add `is_unaligned` to the metamap (note the use of `+` to create a copy of `meta`
-    // to avoid modifying every item in the channel;
-    // https://github.com/nextflow-io/nextflow/issues/2660)
-    | map { meta, paths, is_unaligned -> [meta + [is_unaligned: is_unaligned], paths] }
     | branch { meta, paths ->
         // set `paths` to `null` for uBAM samples if unallowed (they will be added to
         // the results channel in shape of `[meta, null]` at the end of the function
@@ -245,7 +241,12 @@ process checkBamHeaders {
     output:
         // set the two env variables by `eval`-ing the output of the python script
         // checking the XAM headers
-        tuple val(meta), env(IS_UNALIGNED), env(MIXED_HEADERS)
+        tuple(
+            val(meta),
+            path("input_dir/reads*.bam", includeInputs: true),
+            env(IS_UNALIGNED),
+            env(MIXED_HEADERS),
+        )
     script:
     """
     workflow-glue check_bam_headers_in_dir input_dir > env.vars
@@ -306,14 +307,18 @@ process bamstats {
     input:
         tuple val(meta), path("reads.bam")
     output:
-        tuple val(meta), path("reads.bam"), path("bamstats_results")
+        tuple val(meta),
+              path("reads.bam"),
+              path("bamstats_results")
     script:
         def bamstats_threads = Math.max(1, task.cpus - 1)
     """
     mkdir bamstats_results
     bamstats reads.bam -s $meta.alias -u \
         -f bamstats_results/bamstats.flagstat.tsv -t $bamstats_threads \
+        --histograms histograms \
     | bgzip > bamstats_results/bamstats.readstats.tsv.gz
+    mv histograms/* bamstats_results/
 
     # extract the run IDs from the per-read stats
     csvtk cut -tf runid bamstats_results/bamstats.readstats.tsv.gz \
@@ -450,7 +455,9 @@ process fastcat {
         tuple val(meta), path("input")
         val extra_args
     output:
-        tuple val(meta), path("seqs.fastq.gz"), path("fastcat_stats")
+        tuple val(meta),
+              path("seqs.fastq.gz"),
+              path("fastcat_stats")
     script:
         String out = "seqs.fastq.gz"
         String fastcat_stats_outdir = "fastcat_stats"
@@ -460,10 +467,12 @@ process fastcat {
             -s ${meta["alias"]} \
             -r >(bgzip -c > $fastcat_stats_outdir/per-read-stats.tsv.gz) \
             -f $fastcat_stats_outdir/per-file-stats.tsv \
+            --histograms histograms \
             $extra_args \
             input \
             | bgzip > $out
 
+        mv histograms/* $fastcat_stats_outdir
         # extract the run IDs from the per-read stats
         csvtk cut -tf runid $fastcat_stats_outdir/per-read-stats.tsv.gz \
         | csvtk del-header | sort | uniq > $fastcat_stats_outdir/run_ids

nextflow.config

@@ -105,7 +105,7 @@ params {
       ]
     agent = null
     container_sha = "shae7c9f184996a384e99be68e790f0612f0c732867"
-    common_sha = "sha91452ece4f647f62b32dac3a614635a6f0d7f8b5"
+    common_sha = "sha399b89c275a4d8eac477a415691cb93180661be6"
     }
 }
 
@@ -173,7 +173,7 @@ profiles {
                 container = "${params.aws_image_prefix}-wf-transcriptomes:${params.wf.container_sha}-root"
             }
             withLabel:wf_common {
-                container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}-root"
+                container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"
             } 
             shell = ['/bin/bash', '-euo', 'pipefail']
         }