refactor: Increase parameterization in preprocess and host-removal (#31)

* refactor: Remove host check for preprocess * feat: Add skip host removal * feat: Add flag to skip preprocess * refactor: Also skip fastx with skip preprocess * fix: Remove repeated line * docs: Add host removal to schema
dalmolingroup · Mar 24, 2024 · fc6877c · fc6877c
1 parent 9d85097
commit fc6877c
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Showing 4 changed files with 36 additions and 16 deletions.
diff --git a/docs/params.md b/docs/params.md
@@ -23,6 +23,7 @@ Choose to skip pipeline steps
 | `skip_classification` | Skip taxonomic classification | `boolean` |  |  |  |
 | `skip_alignment` | Skip alignment | `boolean` |  |  |  |
 | `skip_functional` | Skip functional annotation | `boolean` |  |  |  |
+| `skip_host_removal` | Skip host removal | `boolean` |  |  |  |
 
 ## Decontamination
 

diff --git a/nextflow.config b/nextflow.config
@@ -43,6 +43,7 @@ params {
     maximum_evalue             = 0.0001
 
     // Skips
+    skip_host_removal          = false
     skip_classification        = false
     skip_functional            = false
     skip_alignment             = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": [
+                "input",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -66,6 +69,11 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-database",
                     "description": "Skip functional annotation"
+                },
+                "skip_host_removal": {
+                    "type": "boolean",
+                    "description": "Skip host removal",
+                    "fa_icon": "fab fa-ioxhost"
                 }
             },
             "fa_icon": "fas fa-angle-double-right"
@@ -136,7 +144,9 @@
                     "description": "Run Kraken2 classifier"
                 }
             },
-            "required": ["kaiju_db"],
+            "required": [
+                "kaiju_db"
+            ],
             "fa_icon": "fab fa-pagelines"
         },
         "functional": {
@@ -170,7 +180,9 @@
                     "description": "Maximum evalue of a match to be used for annotation"
                 }
             },
-            "required": ["id_mapping"],
+            "required": [
+                "id_mapping"
+            ],
             "fa_icon": "fas fa-gavel"
         },
         "assembly": {
@@ -278,7 +290,14 @@
                     "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": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -394,4 +413,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}
diff --git a/workflows/euryale.nf b/workflows/euryale.nf
@@ -73,9 +73,9 @@ def multiqc_report = []
 
 workflow EURYALE {
     if (params.reference_fasta == null && params.diamond_db == null) { exit 1, 'A reference fasta (--reference_fasta) or a DIAMOND db (--diamond_db) must be specified' }
-    if (params.host_fasta == null && params.bowtie2_db == null) {exit 1, 'Either a host reference FASTA (--host_fasta) or a pre-built bowtie2 index (--bowtie2_db) must be specified'}
     if (params.run_kaiju == true && params.kaiju_db == null) {exit 1, 'A Kaiju tar.gz database must be specified with --kaiju_db'}
     if (params.run_kraken2 == true && params.kraken2_db == null) {exit 1, 'A Kraken2 database must be specified with --kraken2_db'}
+    if (params.host_fasta == null && params.bowtie2_db == null && params.skip_host_removal == false) {exit 1, 'Either a host reference FASTA (--host_fasta) or a pre-built bowtie2 index (--bowtie2_db) must be specified'}
 
     ch_versions = Channel.empty()
     ch_kraken_db = params.run_kraken2 ? file(params.kraken2_db) : []
@@ -96,19 +96,18 @@ workflow EURYALE {
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
     INPUT_CHECK.out.reads.set { reads }
 
-    PREPROCESS (
-        reads
-    )
-    ch_versions = ch_versions.mix(PREPROCESS.out.versions)
+    if (params.skip_preprocess) {
+        clean_reads = reads
+    } else {
+        PREPROCESS (
+            reads
+        )
+        ch_versions = ch_versions.mix(PREPROCESS.out.versions)
 
-    if (ch_host_reference) {
         PREPROCESS.out.reads
             .set { clean_reads }
-    } else {
-        PREPROCESS.out.merged_reads
-            .set { clean_reads }
+        ch_multiqc_files = ch_multiqc_files.mix(PREPROCESS.out.multiqc_files.collect())
     }
-    ch_multiqc_files = ch_multiqc_files.mix(PREPROCESS.out.multiqc_files.collect())
 
     if (ch_host_reference || ch_bowtie2_db) {
         HOST_REMOVAL (
@@ -132,7 +131,7 @@ workflow EURYALE {
         ch_versions = ch_versions.mix(ASSEMBLY.out.versions)
     }
 
-    if (!params.assembly_based) {
+    if (!params.assembly_based && !params.skip_preprocess) {
         GUNZIP (
             clean_reads
         )