Add final adapterremoval options to match fastp functionality

conf/modules.config

@@ -62,18 +62,15 @@ process {
         ]
     }
 
-    withName: FASTP {
+    withName: FASTP_SINGLE {
-        ext.prefix = { "${meta.id}_${meta.run_accession}" }
         ext.args   = [
-            // collapsing options - option to retain singletons
-            params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
             // trimming options
             params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
             params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
-            !{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
             // filtering options
             "--length_required ${params.shortread_clipmerge_minlength}"
         ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/fastp" },
             mode: 'copy',
@@ -81,6 +78,61 @@ process {
         ]
     }
 
+    withName: FASTP_PAIRED {
+        ext.args   = [
+            // collapsing options - option to retain singletons
+            params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
+            // trimming options
+            params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
+            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
+            params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
+            // filtering options
+            "--length_required ${params.shortread_clipmerge_minlength}"
+        ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/fastp" },
+            mode: 'copy',
+            pattern: '*.fastq.gz'
+        ]
+    }
+
+    withName: ADAPTERREMOVAL_SINGLE {
+        ext.args   = [
+            // trimming options
+            params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
+            params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
+            // filtering options
+            "--minlength ${params.shortread_clipmerge_minlength}"
+        ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/adapterremoval" },
+            mode: 'copy',
+            pattern: '*.fastq.gz'
+        ]
+    }
+
+    withName: ADAPTERREMOVAL_PAIRED {
+        ext.args   = [
+            // collapsing options
+            params.shortread_clipmerge_mergepairs ? "--collapse" : "",
+            // trimming options
+            params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
+            params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
+            params.shortread_clipmerge_adapter2 ? "--adapter2 ${params.shortread_clipmerge_adapter2}" : "",
+            // filtering options
+            "--minlength ${params.shortread_clipmerge_minlength}"
+        ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            path: { "${params.outdir}/adapterremoval" },
+            mode: 'copy',
+            pattern: '*.fastq.gz'
+        ]
+    }
+
+
     withName: PORECHOP {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
@@ -99,23 +151,23 @@ process {
     }
 
     withName: MALT_RUN {
+        ext.args = { "${meta.db_params}" }
+        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/malt/${meta.db_name}" },
             mode: 'copy',
             pattern: '*.{rma6,tab,text,sam,log}'
         ]
-        ext.args = { "${meta.db_params}" }
-        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
     }
 
     withName: KRAKEN2_KRAKEN2 {
+        ext.args = { "${meta.db_params}" }
+        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
             mode: 'copy',
             pattern: '*.{fastq.gz,txt}'
         ]
-        ext.args = { "${meta.db_params}" }
-        ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
     }
 
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {

nextflow.config

@@ -59,7 +59,7 @@ params {
     shortread_clipmerge_tool                = 'fastp'
     shortread_clipmerge_skipadaptertrim     = false
     shortread_clipmerge_mergepairs          = false
-    shortread_clipmerge_excludeunmerged     = true
+    shortread_clipmerge_excludeunmerged     = false
     shortread_clipmerge_adapter1            = null
     shortread_clipmerge_adapter2            = null
     shortread_clipmerge_minlength           = 15

nextflow_schema.json

@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
+            "required": ["input", "outdir"],
-                "input",
-                "outdir"
-            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -176,14 +173,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -277,7 +267,7 @@
         },
         "shortread_clipmerge_excludeunmerged": {
             "type": "boolean",
-            "default": true
+            "default": false
         },
         "longread_clip": {
             "type": "boolean"
@@ -295,10 +285,7 @@
         "shortread_clipmerge_tool": {
             "type": "string",
             "default": "fastp",
-            "enum": [
+            "enum": ["fastp", "adapterremoval"]
-                "fastp",
-                "adapterremoval"
-            ]
         },
         "shortread_clipmerge_skipadaptertrim": {
             "type": "boolean"

subworkflows/local/shortread_adapterremoval.nf

@@ -16,7 +16,6 @@ workflow SHORTREAD_ADAPTERREMOVAL {
     ch_multiqc_files      = Channel.empty()
 
     ch_input_for_adapterremoval = reads
-                                    .dump(tag: "pre_adapterremoval_branch")
                                     .branch{
                                         single: it[0]['single_end'] == true
                                         paired: it[0]['single_end'] == false
@@ -36,11 +35,13 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                                                 .map {
                                                     meta, reads ->
                                                         def meta_new = meta.clone()
-                                                        meta_new['single_end'] = 1
+                                                        meta_new['single_end'] = true
 
                                                         [ meta_new, reads ]
                                                     }
                                                     .groupTuple(by: 0)
+
+
         ch_adapterremoval_reads_prepped_pe = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
 
         ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
@@ -51,7 +52,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                                                     .map {
                                                         meta, reads ->
                                                             def meta_new = meta.clone()
-                                                            meta_new['single_end'] = 1
+                                                            meta_new['single_end'] = true
 
                                                             [ meta_new, reads ]
                                                         }
@@ -65,13 +66,10 @@ workflow SHORTREAD_ADAPTERREMOVAL {
 
         ch_adapterremoval_reads_prepped_pe = ADAPTERREMOVAL_PAIRED.out.pair1_truncated
                                                 .join( ADAPTERREMOVAL_PAIRED.out.pair2_truncated )
-                                                .dump(tag: "pre-group")
                                                 .groupTuple(by: 0)
-                                                .dump(tag: "post-group")
                                                 .map { meta, pair1, pair2 ->
                                                         [ meta, [ pair1, pair2 ].flatten() ]
                                                 }
-                                                .dump(tag: "post-map")
 
 
         ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe