Update aligners (bwa, bowtie2, chromap and star)

CHANGELOG.md

@@ -70,6 +70,11 @@ the last release have been listed below for reference.
 | python                      | 3.8.3       | 3.12.12     |
 | multiqc                     | 1.25.1      | 1.33        |
 | deeptools                   | 3.5.5       | 3.5.6       |
+| bowtie2                     | 2.5.2       | 2.5.4       |
+| picard                      | 3.2.0       | 3.4.0       |
+| samtools                    | 1.15.1      | 1.20        |
+| bwa                         | 0.7.18      | 0.7.19      |
+| chromap                     | 0.2.6       | 0.3.2       |
 |                             |             |             |
 
 ## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-07

conf/modules.config

@@ -26,8 +26,7 @@ process {
         ext.args   = 'samplesheet.valid.csv'
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
@@ -60,7 +59,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_reference
         ]
     }
@@ -78,7 +76,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: params.save_reference
         ]
     }
@@ -227,19 +224,32 @@ process {
     withName: 'CHROMAP_INDEX' {
         publishDir = [
             path: { "${params.outdir}/genome/index/${params.aligner}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
-    withName: CHROMAP_CHROMAP {
+    withName: 'CHROMAP_CHROMAP' {
         ext.args   = '-l 2000 --low-mem --SAM'
         ext.args3  = { meta.read_group ? "-r ${meta.read_group}" : '' }
         ext.prefix = { "${meta.id}.Lb" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/library" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: false
+        ]
+    }
+
+    withName: '.*:FASTQ_ALIGN_CHROMAP:PICARD_ADDORREPLACEREADGROUPS' {
+        ext.args = {
+            [
+                meta.read_group ? "--RGID ${meta.id} --RGSM ${meta.id - ~/_T\d+$/} --RGPL ILLUMINA --RGLB ${meta.id} --RGPU 1" : '',
+                params.seq_center ? "--RGCN ${params.seq_center}" : ''
+            ].join(' ').trim()
+        }
+        ext.prefix = { "${meta.id}.Lb.updated_readgroups" }
+        publishDir = [
+            path: { "${params.outdir}/${params.aligner}/library" },
+            mode: params.publish_dir_mode,
             enabled: false
         ]
     }
@@ -424,8 +434,7 @@ process {
     withName: 'MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS' {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/merged_library/phantompeakqualtools" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
@@ -575,7 +584,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/qc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -646,8 +654,7 @@ process {
         ext.prefix = { "${meta.id}.consensus_peaks" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
@@ -666,8 +673,7 @@ process {
         ext.prefix = { "${meta.id}.consensus_peaks" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/merged_library/macs3/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}/consensus/${meta.id}/deseq2" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 
@@ -698,8 +704,7 @@ process {
         ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
         publishDir = [
             path: { "${params.outdir}/multiqc/${params.narrow_peak ? 'narrow_peak' : 'broad_peak'}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            mode: params.publish_dir_mode
         ]
     }
 }

modules.json

@@ -12,7 +12,7 @@
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "92b8df948fd8cdb223e051f5f5e414818a073ee0",
+                        "git_sha": "0cd85f32cf1a1828205b16e4267277ba9457570b",
                         "installed_by": ["fastq_align_bowtie2", "modules"]
                     },
                     "bowtie2/build": {
@@ -27,12 +27,12 @@
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "707241c72951f24fd89982c4c80c5983a4c437ef",
+                        "git_sha": "2fb127c8fd13de0adaa676df7169131e45c0b114",
                         "installed_by": ["fastq_align_bwa", "modules"]
                     },
                     "chromap/chromap": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "f2f969a4ee32243c7fab75f341f9be1dd3ce1a23",
                         "installed_by": ["fastq_align_chromap", "modules"],
                         "patch": "modules/nf-core/chromap/chromap/chromap-chromap.diff"
                     },
@@ -101,14 +101,37 @@
                         "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
+                    "picard/addorreplacereadgroups": {
+                        "branch": "master",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "installed_by": [
+                            "_",
+                            "a",
+                            "c",
+                            "f",
+                            "g",
+                            "h",
+                            "i",
+                            "l",
+                            "m",
+                            "n",
+                            "o",
+                            "p",
+                            "q",
+                            "r",
+                            "s",
+                            "t",
+                            "fastq_align_chromap"
+                        ]
+                    },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
                         "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["bam_markduplicates_picard", "modules"]
                     },
                     "picard/mergesamfiles": {
@@ -128,28 +151,27 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
-                        "installed_by": ["bam_stats_samtools", "modules"],
-                        "patch": "modules/nf-core/samtools/flagstat/samtools-flagstat.diff"
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "fe93fde0845f907fc91ad7cc7d797930408824df",
+                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "subread/featurecounts": {
@@ -188,32 +210,32 @@
                 "nf-core": {
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
+                        "git_sha": "1298fbd2004c2913d6682ce4a419647d97a8fc3f",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "7ac6cbe7c17c2dad685da7f70496c8f48ea48687",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_chromap"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "7ac6cbe7c17c2dad685da7f70496c8f48ea48687",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
                     },
                     "fastq_align_bowtie2": {
                         "branch": "master",
-                        "git_sha": "9afa0584136287aa20fc18296f45f103c0c4e69a",
+                        "git_sha": "a0961c41021561ac7cf139f86bd7812a2f99e994",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_bwa": {
                         "branch": "master",
-                        "git_sha": "9afa0584136287aa20fc18296f45f103c0c4e69a",
+                        "git_sha": "cbb7a6362981f07d2c26e43f8186025320569ffd",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_chromap": {
                         "branch": "master",
-                        "git_sha": "9afa0584136287aa20fc18296f45f103c0c4e69a",
+                        "git_sha": "d92e0f8276a79d316fd324eae0edefeaf680804c",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {