Replace local blat for nf-core blat in contaminant filter subworkflow

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#388]](https://github.com/nf-core/smrnaseq/pull/388) - Fix [igenomes fix](https://github.com/nf-core/smrnaseq/issues/360) - Fix workflow scripts so that they can use igenome parameters.
 - [[#391]](https://github.com/nf-core/smrnaseq/pull/391) - Fix [error because of large chromosomes](https://github.com/nf-core/smrnaseq/issues/132) - Change `.bai` index for `.csi` index in `samtools_index` to fix .
 - [[#392]](https://github.com/nf-core/smrnaseq/pull/392) - Update [Reduce tests](https://github.com/nf-core/smrnaseq/issues/389) - Combine and optimize tests, and reduce samplesheets sizes.
+- [[#397]](https://github.com/nf-core/smrnaseq/pull/397) - Fix [contaminant filter failure because of the Docker image for BLAT](https://github.com/nf-core/smrnaseq/issues/354) - Improvements to contaminant filter subworkflow and replacement for nf-core modules.
 - [[#398]](https://github.com/nf-core/smrnaseq/pull/398) - Update [Input channels](https://github.com/nf-core/smrnaseq/issues/390) - Updated channel and params handling through workflows.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

conf/modules.config

@@ -201,6 +201,24 @@ process {
         ]
     }
 
+    withName: 'NFCORE_SMRNASEQ:CONTAMINANT_FILTER:BLAT.*' {
+        ext.args = '-out=blast8'
+        ext.prefix = {"${meta.id}_${meta2.id}"}
+        tag = {"${meta.id} ${meta2.id}"}
+        publishDir = [ enabled: false ]
+    }
+
+    withName: 'NFCORE_SMRNASEQ:CONTAMINANT_FILTER:GAWK.*' {
+        ext.prefix = {"significant_hits_${meta.id}"}
+        publishDir = [ enabled: false ]
+    }
+
+    withName: 'NFCORE_SMRNASEQ:CONTAMINANT_FILTER:SEQKIT_GREP.*' {
+        ext.prefix = {"filtered_${meta.id}"}
+        ext.args = '-v'
+        publishDir = [ enabled: false ]
+    }
+
     //
     // MIRNA_QUANT
     //

modules.json

@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "blat": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805",
@@ -25,6 +30,11 @@
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
+                    "gawk": {
+                        "branch": "master",
+                        "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
@@ -55,6 +65,12 @@
                         "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
+                    "seqkit/grep": {
+                        "branch": "master",
+                        "git_sha": "03fbf6c89e551bd8d77f3b751fb5c955f75b34c5",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/seqkit/grep/seqkit-grep.diff"
+                    },
                     "umicollapse": {
                         "branch": "master",
                         "git_sha": "18e452a645bd56d1a539f53c7656e3d2915246f7",