Fixes on modules

README.md

@@ -91,9 +91,16 @@ Optional arguments include:
 ```
 
 Use `--core_mode true` for large catalogues like the mouse-gut to avoid over-prediction due to an extremely large number of accessory genes in the pangenome.
-Nextflow option `-profile` can be use to select a suitable config for your computational resources.
+Nextflow option `-profile` can be use to select a suitable config for your computational resources. You can add profile files to the `config` directory.
 Nextflow option `-resume` can be use to re-run the pipeline from the last successfully finished step.
 
+
+## Test
+
+To test the pipeline you can run...
+
+
+
 ## Credits
 
 ebi-metagenomics/shallowmapping pipeline was originally written by @Ales-ibt.

main.nf

@@ -21,7 +21,7 @@ include { validateParameters; paramsHelp } from 'plugin/nf-validation'
 if (params.help) {
     def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
     def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --biome <BIOME> -profile docker"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
 }

modules/local/align/bwamem2.nf

@@ -2,7 +2,6 @@ process ALIGN_BWAMEM2 {
     tag "$meta.id"
     label 'process_high'
 
-    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' :
         'biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:2d15960ccea84e249a150b7f5d4db3a42fc2d6c3-0' }"
@@ -13,25 +12,23 @@ process ALIGN_BWAMEM2 {
 
     output:
     tuple val(meta), path("*_sorted.bam"), path("*_sorted.bam.bai"), emit: bam
-    path  "versions.yml"                 , emit: versions
+    path  "versions.yml"                                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = '-M'
-    def args2 = '-F256 -F4 -uS'
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
 
     bwa-mem2 \\
         mem \\
-        $args \\
+        -M \\
         -t $task.cpus \\
         \$INDEX \\
         $reads \\
-        | samtools view -@ ${task.cpus} $args2 - \\
+        | samtools view -@ ${task.cpus} -F256 -F4 -uS - \\
         | samtools sort -@ ${task.cpus} -O bam - -o ${prefix}_sorted.bam
     samtools index -@ ${task.cpus} ${prefix}_sorted.bam
 
@@ -46,6 +43,7 @@ process ALIGN_BWAMEM2 {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
+    touch ${prefix}.bam.bai
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')

modules/local/dram/distill.nf

@@ -14,7 +14,7 @@ process DRAM_DISTILL {
     val(in_type)    //species or community
 
     output:
-    tuple val(meta), path("*_dram.*"), emit: destill_out
+    tuple val(meta), path("*_dram*"), emit: destill_out
     path "versions.yml"              , emit: versions
 
     when:
@@ -27,23 +27,17 @@ process DRAM_DISTILL {
 
     """
     if [[ "${in_type}" == "community" ]]; then
-        echo ",fasta,scaffold,gene_position,start_position,end_position,strandedness,rank,kegg_id,kegg_hit,pfam_hits,cazy_hits,bin_taxonomy" | sed 's/,/\t/g' > community_input.txt
-        cat $dram_summary >> community_input.txt  
-        DRAM.py \\
-            distill \\
-            -i community_input.txt  \\
-            -o dram_out
-        mv dram_out/product.html ${prefix}_${tool}_${in_type}_dram.html
-        mv dram_out/product.tsv ${prefix}_${tool}_${in_type}_dram.tsv
-    else
-        DRAM.py \\
-            distill \\
-            -i $dram_summary  \\
-            -o dram_out
-        mv dram_out/product.html ${prefix}_${tool}_${in_type}_dram.html
-        mv dram_out/product.tsv ${prefix}_${tool}_${in_type}_dram.tsv
+        echo ",fasta,scaffold,gene_position,start_position,end_position,strandedness,rank,kegg_id,kegg_hit,pfam_hits,cazy_hits,bin_taxonomy" | sed 's/,/\t/g' > dram_input.txt
     fi
 
+    cat $dram_summary >> dram_input.txt  
+    DRAM.py \\
+        distill \\
+        -i dram_input.txt  \\
+        -o dram_out
+    mv dram_out/product.html ${prefix}_${tool}_${in_type}_dram.html
+    mv dram_out/product.tsv ${prefix}_${tool}_${in_type}_dram.tsv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         dram: $VERSION