Start adding conditions in modules.conf - non-cat not working

conf/modules.config

@@ -71,6 +71,12 @@ process {
                 path: { "${params.outdir}/fastp" },
                 mode: params.publish_dir_mode,
                 pattern: '*.{log,html,json}'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
             ]
         ]
     }
@@ -99,6 +105,12 @@ process {
                 path: { "${params.outdir}/fastp" },
                 mode: params.publish_dir_mode,
                 pattern: '*.{log,html,json}'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
             ]
         ]
     }
@@ -122,6 +134,12 @@ process {
                 path: { "${params.outdir}/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.settings'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
             ]
         ]
     }
@@ -148,6 +166,12 @@ process {
                 path: { "${params.outdir}/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.settings'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
             ]
         ]
     }
@@ -166,6 +190,7 @@ process {
                 mode: params.publish_dir_mode,
                 pattern: '*.log'
             ]
+            // TODO ANALYSIS READY
         ]
     }
 
@@ -190,14 +215,78 @@ process {
                 pattern: '*.log'
             ]
         ]
+        // TODO ANALYSIS READY
+    }
+
+    withName: BBMAP_BBDUK {
+        ext.args =  [
+                "entropy=${params.shortread_complexityfilter_entropy}",
+                "entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
+                params.shortread_complexityfilter_bbduk_mask ?  "entropymask=t" : "entropymask=f"
+            ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            [
+                path: { "${params.outdir}/bbduk/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.{fastq.gz,log}',
+                enabled: params.save_complexityfiltered_reads
+            ],
+            [
+                path: { "${params.outdir}/bbduk/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_reads
+            ]
+        ]
+    }
+
+    withName: PRINSEQPLUSPLUS {
+        ext.args =  [
+                params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
+                "-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
+            ].join(' ').trim()
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
+        publishDir = [
+            [
+                path: { "${params.outdir}/prinseqplusplus/" },
+                mode: params.publish_dir_mode,
+                pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
+                enabled: params.save_complexityfiltered_reads
+            ],
+            [
+                path: { "${params.outdir}/prinseqplusplus/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && params.shortread_complexityfilter_tool && params.save_analysis_ready_reads
+            ]
+        ]
     }
 
     withName: BOWTIE2_BUILD {
         publishDir = [
+            [
             path: { "${params.outdir}/bowtie2/build" },
             mode: params.publish_dir_mode,
             pattern: 'bowtie2',
             enabled: params.save_hostremoval_index
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && !params.perform_shortread_qc && params.save_analysis_ready_reads
+            ]
         ]
     }
 
@@ -221,6 +310,12 @@ process {
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.save_hostremoval_unmapped
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                saveAs: { (( !params.perform_runmerging | params.perform_runmerging && !${meta.is_multirun} ) && params.perform_shortread_hostremoval && params.save_analysis_ready_reads ) ? it : null }
             ]
         ]
     }
@@ -243,6 +338,7 @@ process {
             pattern: '*.bam',
             enabled: params.save_hostremoval_bam
         ]
+        // TODO ANALYSIS READY READS
     }
 
     withName: SAMTOOLS_VIEW {
@@ -269,56 +365,21 @@ process {
         ]
     }
 
-    withName: BBMAP_BBDUK {
-        ext.args =  [
-                "entropy=${params.shortread_complexityfilter_entropy}",
-                "entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
-                params.shortread_complexityfilter_bbduk_mask ?  "entropymask=t" : "entropymask=f"
-            ].join(' ').trim()
-        ext.prefix = { "${meta.id}_${meta.run_accession}" }
-        publishDir = [
-            [
-                path: { "${params.outdir}/bbduk/" },
-                mode: params.publish_dir_mode,
-                pattern: '*.{fastq.gz,log}',
-                enabled: params.save_complexityfiltered_reads
-            ],
-            [
-                path: { "${params.outdir}/bbduk/" },
-                mode: params.publish_dir_mode,
-                pattern: '*.log'
-            ]
-        ]
-    }
-
-    withName: PRINSEQPLUSPLUS {
-        ext.args =  [
-                params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
-                "-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
-            ].join(' ').trim()
-        ext.prefix = { "${meta.id}_${meta.run_accession}" }
-        publishDir = [
-            [
-                path: { "${params.outdir}/prinseqplusplus/" },
-                mode: params.publish_dir_mode,
-                pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
-                enabled: params.save_complexityfiltered_reads
-            ],
-            [
-                path: { "${params.outdir}/prinseqplusplus/" },
-                mode: params.publish_dir_mode,
-                pattern: '*.log'
-            ]
-        ]
-    }
-
     withName: CAT_FASTQ {
         ext.prefix = { "${meta.id}" }
         publishDir = [
+            [
                 path: { "${params.outdir}/run_merging/" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
                 enabled: params.save_runmerged_reads
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_reads" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.perform_runmerging && params.save_analysis_ready_reads
+            ]
         ]
     }
 

nextflow.config

@@ -105,6 +105,8 @@ params {
     save_hostremoval_bam                    = false
     save_hostremoval_unmapped              = false
 
+    // Publishing final reads going into profiling
+    save_analysis_ready_reads = false
 
     // MALT
     run_malt                   = false

subworkflows/local/input_check.nf

@@ -43,7 +43,6 @@ workflow INPUT_CHECK {
     // Channel generation
     ch_fastq = ch_parsed_samplesheet.fastq
         .map { create_fastq_channel(it) }
-        .dump(tag: "boop") 
 
     ch_nanopore = ch_parsed_samplesheet.nanopore
         .map { create_fastq_channel(it) }