Merge branch 'master-html-creation-with-timestamps' of github.com:SMD…

…-Bioinformatics-Lund/gms_16S into master-html-creation-with-timestamps

conf/modules.config

@@ -157,7 +157,7 @@ process {
                 path: { "${params.outdir}/results" },
                 mode: params.publish_dir_mode,
                 overwrite: params.publish_dir_overwrite,
-                pattern: '*{.fa}',
+                pattern: '*.{fastq_unclassified_mapped.fasta,fastq_unmapped.fasta}',
                 enabled: params.output_unclassified
             ],
 

modules/local/emu/abundance/main.nf

@@ -18,10 +18,10 @@ process EMU_ABUNDANCE {
 
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    conda "bioconda::emu=3.4.4"
+    conda "bioconda::emu=3.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/emu:3.4.4--hdfd78af_1':
-        'quay.io/biocontainers/emu:3.4.4--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/emu:3.5.1--hdfd78af_0':
+        'quay.io/biocontainers/emu:3.5.1--hdfd78af_0' }"
 
     input:
     //  Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
@@ -37,8 +37,8 @@ process EMU_ABUNDANCE {
     tuple val(meta), path("*read-assignment-distributions.tsv"), emit: assignment_report, optional:true
     path "versions.yml"           , emit: versions
     tuple val(meta), path("*.sam"), emit: samfile, optional:true
-    tuple val(meta), path("*.fa"), emit: unclassified_fa , optional:true
-
+    tuple val(meta), path("*.fastq_unclassified_mapped.fasta"), emit: unclassified_mapped_fa , optional:true
+    tuple val(meta), path("*.fastq_unmapped.fasta"), emit: unclassified_unmapped_fa , optional:true
 
 
     when:

modules/local/emu/abundance/meta.yml

@@ -54,6 +54,17 @@ output:
       type: file
       description: File containing alignment data
       pattern: "*{.sam}
+  //unclassified and mapped fasta file
+  - unclassified_fa
+      type: file
+      description: File containing reads that mapped to the database but was presumed to be not in the sample by EMU´s algorithm. 
+      pattern: "*{.fastq_unclassified_mapped.fasta}
+  //unmapped fasta file
+  - unclassified_unmapped_fa
+      type: file
+      description: File containing reads that was not mapped to the database. 
+      pattern: "*{.fastq_unmapped.fasta}
+
 
   # emu log. Put on ice.
  // - emulog