General cleanup

CHANGELOG.md

@@ -39,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#439]](https://github.com/nf-core/smrnaseq/pull/439) - Fix [Fix paired end samples processing](https://github.com/nf-core/smrnaseq/issues/415) - Fix paired end sample handling and add test profile.
 - [[#441]](https://github.com/nf-core/smrnaseq/pull/441) - Migrate [local contaminant bowtie to nf-core](https://github.com/nf-core/smrnaseq/issues/436) - Replace local processes with `BOWTIE2_ALIGN`.
 - [[#443]](https://github.com/nf-core/smrnaseq/pull/443) - Migrate [mirna and genome_quant bowtie to nf-core](https://github.com/nf-core/smrnaseq/issues/436) - Replace local processes with `BOWTIE_ALIGN`.
+- [[#447]](https://github.com/nf-core/smrnaseq/pull/447) - Fix [Minor fixes and general pipeline cleanup](https://github.com/nf-core/smrnaseq/issues/400) - Update variable and processes names, update channel comments, remove unused modules and params.
 - [[#448]](https://github.com/nf-core/smrnaseq/pull/448) - Migrate local mirdeep to [nf-core mirdeep2 modules and subworkflow](https://github.com/nf-core/smrnaseq/issues/443) and generate [test profile for mirdeep2](https://github.com/nf-core/smrnaseq/issues/399).
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch

conf/modules.config

@@ -479,7 +479,7 @@ process {
     }
 
 
-    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:TABLE_MERGE' {
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:DATATABLE_MERGE' {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/mirtop" },
             mode: params.publish_dir_mode,

conf/test.config

@@ -28,7 +28,6 @@ params {
     mirtrace_species         = 'hsa'
     skip_mirdeep             = true
     save_merged              = false
-    save_aligned_mirna_quant = false
 
 }
 

conf/test_contamination.config

@@ -27,7 +27,6 @@ params {
     mirtrace_species         = 'hsa'
     skip_mirdeep             = true
     save_merged              = false
-    save_aligned_mirna_quant = false
 
 
     filter_contamination = true

main.nf

@@ -78,7 +78,9 @@ workflow {
         params.monochrome_logs,
         args,
         params.outdir,
-        params.input
+        params.input,
+        params.three_prime_adapter,
+        params.phred_offset
     )
 
     //
@@ -102,6 +104,8 @@ workflow {
         PREPARE_GENOME.out.other_contamination,
         ch_versions,
         PIPELINE_INITIALISATION.out.samplesheet,
+        PIPELINE_INITIALISATION.out.three_prime_adapter,
+        PIPELINE_INITIALISATION.out.phred_offset
     )
 
     //

modules.json

@@ -36,11 +36,6 @@
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     },
-                    "cat/cat": {
-                        "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
-                        "installed_by": ["modules"]
-                    },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
@@ -106,11 +101,6 @@
                         "git_sha": "7c316cae26baf55e0add993bed2b0c9f7105c653",
                         "installed_by": ["modules"]
                     },
-                    "pigz/uncompress": {
-                        "branch": "master",
-                        "git_sha": "c00055a0b13d622b4f1f51a8e5be31deaf99ded7",
-                        "installed_by": ["modules"]
-                    },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
@@ -169,7 +159,7 @@
                     },
                     "untarfiles": {
                         "branch": "master",
-                        "git_sha": "958e4a6031deefa327f339f11d9baf1ab5a32d5f",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }

modules/local/datatable_merge/datatable_merge.nf → modules/local/datatable_merge/main.nf

@@ -1,4 +1,4 @@
-process TABLE_MERGE {
+process DATATABLE_MERGE {
     label 'process_medium'
 
     conda 'conda-forge::r-data.table=1.12.2'

modules/local/datatable_merge/tests/datatable_merge.nf.test

@@ -1,11 +1,11 @@
 nextflow_process {
 
-    name "Test Process TABLE_MERGE"
-    script "../datatable_merge.nf"
-    process "TABLE_MERGE"
+    name "Test Process DATATABLE_MERGE"
+    script "../main.nf"
+    process "DATATABLE_MERGE"
     tag "modules"
     tag "modules_local"
-    tag "table_merge"
+    tag "datatable_merge"
 
     test("Contains hsa-miR-365b-3p, hsa-miR-7-5p, hsa-miR-103a-3p") {
 
@@ -15,7 +15,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [file("https://github.com/nf-core/test-datasets/raw/smrnaseq/nf-test_data/datatable_merge/small_mirtop_dataset.txt", checkIfExists: true)]
+                input[0] = [[],file("https://github.com/nf-core/test-datasets/raw/smrnaseq/nf-test_data/datatable_merge/small_mirtop_dataset.txt", checkIfExists: true)]
                 """
             }
         }
@@ -46,7 +46,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [file("https://github.com/nf-core/test-datasets/raw/smrnaseq/nf-test_data/datatable_merge/small_mirtop_dataset.txt", checkIfExists: true)]
+                input[0] = [[],file("https://github.com/nf-core/test-datasets/raw/smrnaseq/nf-test_data/datatable_merge/small_mirtop_dataset.txt", checkIfExists: true)]
                 """
             }
         }

modules/local/datatable_merge/tests/datatable_merge.nf.test.snap

@@ -6,21 +6,21 @@
                     "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
                 ],
                 "1": [
-                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                    "versions.yml:md5,13bf3c8bbf1285dfc0ef547dcbb692b2"
                 ],
                 "mirna_tsv": [
                     "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
                 ],
                 "versions": [
-                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                    "versions.yml:md5,13bf3c8bbf1285dfc0ef547dcbb692b2"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-21T14:27:11.151441241"
+        "timestamp": "2024-09-30T12:57:47.129770995"
     },
     "Does not contain hsa-miR-107, hsa-miR-365a-3p": {
         "content": [
@@ -29,20 +29,20 @@
                     "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
                 ],
                 "1": [
-                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                    "versions.yml:md5,13bf3c8bbf1285dfc0ef547dcbb692b2"
                 ],
                 "mirna_tsv": [
                     "mirna.tsv:md5,f59a6aeb15588c43c2977950a1b0a080"
                 ],
                 "versions": [
-                    "versions.yml:md5,3a8ba7faff9d6dadf80e1a1b026acbe1"
+                    "versions.yml:md5,13bf3c8bbf1285dfc0ef547dcbb692b2"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-21T14:27:39.584509005"
+        "timestamp": "2024-09-30T12:57:56.990602055"
     }
 }

modules/local/edger_qc/tests/edger_qc.nf.test

@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test Process EDGER_QC"
-    script "../edger_qc.nf"
+    script "../main.nf"
     process "EDGER_QC"
 
     test("Should not produce MDS plot") {