Fasta index bismark bwameth

CHANGELOG.md

@@ -4,12 +4,15 @@
 
 ### Bug fixes & refactoring
 
-- 🐛 fix fasta gunzip output [#457](https://github.com/nf-core/methylseq/pull/457)
+- 🐛 fix fasta gunzip output [#462](https://github.com/nf-core/methylseq/pull/457)
 - 🐛 fix bismark/align not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457)
 
 ### Pipeline Updates
 
 - 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457)
+- 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/)
+- 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows [#467](https://github.com/nf-core/methylseq/pull/)
+- 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/)
 
 ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
 

main.nf

@@ -15,11 +15,11 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { METHYLSEQ               } from './workflows/methylseq/'
-include { PREPARE_GENOME          } from './subworkflows/local/prepare_genome/'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
+include { FASTA_INDEX_BISMARK_BWAMETH } from './subworkflows/nf-core/fasta_index_bismark_bwameth/main'
+include { METHYLSEQ                   } from './workflows/methylseq/'
+include { PIPELINE_INITIALISATION     } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
+include { PIPELINE_COMPLETION         } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
+include { getGenomeAttribute          } from './subworkflows/local/utils_nfcore_methylseq_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -52,13 +52,13 @@ workflow NFCORE_METHYLSEQ {
     //
     // SUBWORKFLOW: Prepare any required reference genome indices
     //
-    PREPARE_GENOME(
+    FASTA_INDEX_BISMARK_BWAMETH(
         params.fasta,
         params.fasta_index,
         params.bismark_index,
         params.bwameth_index,
     )
-    ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
+    ch_versions = ch_versions.mix(FASTA_INDEX_BISMARK_BWAMETH.out.versions)
 
     //
     // WORKFLOW: Run pipeline
@@ -67,10 +67,10 @@ workflow NFCORE_METHYLSEQ {
     METHYLSEQ (
         samplesheet,
         ch_versions,
-        PREPARE_GENOME.out.fasta,
-        PREPARE_GENOME.out.fasta_index,
-        PREPARE_GENOME.out.bismark_index,
-        PREPARE_GENOME.out.bwameth_index,
+        FASTA_INDEX_BISMARK_BWAMETH.out.fasta,
+        FASTA_INDEX_BISMARK_BWAMETH.out.fasta_index,
+        FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index,
+        FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index,
     )
     emit:
     multiqc_report = METHYLSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html

modules.json

@@ -23,7 +23,7 @@
                     "bismark/genomepreparation": {
                         "branch": "master",
                         "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "modules"]
                     },
                     "bismark/methylationextractor": {
                         "branch": "master",
@@ -48,7 +48,7 @@
                     "bwameth/index": {
                         "branch": "master",
                         "git_sha": "a716d10039f9728f2674f45c33a95b605851ea50",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
@@ -63,7 +63,7 @@
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "modules"]
                     },
                     "methyldackel/extract": {
                         "branch": "master",
@@ -103,7 +103,7 @@
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
@@ -133,12 +133,17 @@
                     "untar": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fasta_index_bismark_bwameth", "modules"]
                     }
                 }
             },
             "subworkflows": {
                 "nf-core": {
+                    "fasta_index_bismark_bwameth": {
+                        "branch": "master",
+                        "git_sha": "e24c9731daae27a4cd0b072f2e50cc8401a492db",
+                        "installed_by": ["subworkflows"]
+                    },
                     "fastq_align_dedup_bismark": {
                         "branch": "master",
                         "git_sha": "af84433c2e619cf28e026d4140b1b8763ae3690b",