Merge pull request #432 from atrigila/upgrade_multiqc

nf-core · Sep 19, 2024 · 395f801 · 395f801
2 parents 61b3738 + db440ff
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#430]](https://github.com/nf-core/smrnaseq/pull/430) - Emit a [warning if paired-end end data is used](https://github.com/nf-core/smrnaseq/issues/423) - pipeline handles SE data
 - [[#427]](https://github.com/nf-core/smrnaseq/pull/427) - Add [nf-core pigz uncompress](https://github.com/nf-core/smrnaseq/issues/422) - replace local `mirdeep_pigz`
 - [[#429]](https://github.com/nf-core/smrnaseq/pull/429) - Make [saving of intermediate files optional](https://github.com/nf-core/smrnaseq/issues/424) - Allows user to choose whether to save intermediate files or not. Replaces several params that referred to the same such as `params.save_aligned` and `params.save_aligned_mirna_quant`.
+- [[#432]](https://github.com/nf-core/smrnaseq/pull/432) - Update [MultiQC to latest version](https://github.com/nf-core/smrnaseq/issues/428) - Include UMIcollapse module in MultiQC.
 
 ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch
 

diff --git a/modules.json b/modules.json
@@ -7,32 +7,32 @@
                 "nf-core": {
                     "blat": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "49852039cccef84bbf5a3c0e069fac81fa3f0202",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     },
                     "mirtop/counts": {
@@ -62,7 +62,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
+                        "git_sha": "7c316cae26baf55e0add993bed2b0c9f7105c653",
                         "installed_by": ["modules"]
                     },
                     "pigz/uncompress": {
@@ -72,27 +72,27 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
+                        "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "seqcluster/collapse": {
@@ -102,23 +102,23 @@
                     },
                     "seqkit/grep": {
                         "branch": "master",
-                        "git_sha": "03fbf6c89e551bd8d77f3b751fb5c955f75b34c5",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/seqkit/grep/seqkit-grep.diff"
                     },
                     "umicollapse": {
                         "branch": "master",
-                        "git_sha": "18e452a645bd56d1a539f53c7656e3d2915246f7",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
                     "untarfiles": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "958e4a6031deefa327f339f11d9baf1ab5a32d5f",
                         "installed_by": ["modules"]
                     }
                 }
@@ -127,7 +127,7 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_mirna_mirtop": {
@@ -137,7 +137,7 @@
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
+                        "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "fastq_fastqc_umitools_fastp": {

diff --git a/modules/nf-core/blat/environment.yml b/modules/nf-core/blat/environment.yml
diff --git a/modules/nf-core/blat/meta.yml b/modules/nf-core/blat/meta.yml
diff --git a/modules/nf-core/blat/tests/main.nf.test b/modules/nf-core/blat/tests/main.nf.test
diff --git a/modules/nf-core/blat/tests/main.nf.test.snap b/modules/nf-core/blat/tests/main.nf.test.snap
diff --git a/modules/nf-core/blat/tests/nextflow.config b/modules/nf-core/blat/tests/nextflow.config
diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml