Merge pull request #128 from nf-core/template-cleanup

nf-core · Jan 30, 2024 · a492c55 · a492c55
2 parents ec24cfb + 6841c45
commit a492c55
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,19 +7,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- [9712163](https://github.com/nf-core/nascent/commit/97121638eb77e175b912ff45a669426e532c5d7f) - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
+- [ec24cfb](https://github.com/nf-core/nascent/commit/ec24cfb2646904bcc78379a071b50b53a855b9a9) - Update pipeline template to [nf-core/tools 2.11.1](https://github.com/nf-core/tools/releases/tag/2.11.1)
+- [15b8ff3](https://github.com/nf-core/nascent/commit/15b8ff31cd43ec2e330ce7958bd6d7d65529b4d3) - Update pipeline template to [nf-core/tools 2.11](https://github.com/nf-core/tools/releases/tag/2.11)
+- [9712163](https://github.com/nf-core/nascent/commit/97121638eb77e175b912ff45a669426e532c5d7f) - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
 
 ## v2.1.1 - 2023-02-17
 
 ### Fixed
 
-- [[#109](https://github.com/nf-core/nascent/pull/109)] - Fixed bug where using AWS igenomes or passing a pre-made index fails because of an update to the module expects them to have a metamap. Generation was still working.
+- [[#109](https://github.com/nf-core/nascent/pull/109)] - Using AWS igenomes or passing a pre-made index fails because of an update to the module expects them to have a metamap. Generation was still working.
 
 ## v2.1.0 - 2023-02-15
 
 ### Added
 
-- [[#94](https://github.com/nf-core/nascent/pull/94)] - Added a second BEDTools intersect step to allow filtering and overlapping in the same workflow.
+- [[#94](https://github.com/nf-core/nascent/pull/94)] - Add a second BEDTools intersect step to allow filtering and overlapping in the same workflow.
 - [[#101](https://github.com/nf-core/nascent/pull/101)] - Initialized nf-test
 
 ### Changed
@@ -37,8 +39,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - DSL2 conversion
-- [[#28](https://github.com/nf-core/nascent/issues/28)] - Added DRAGMAP alignment
-- [[#64](https://github.com/nf-core/nascent/pull/64)] - Added CHM13 igenomes config
+- [[#28](https://github.com/nf-core/nascent/issues/28)] - Add DRAGMAP alignment
+- [[#64](https://github.com/nf-core/nascent/pull/64)] - Add CHM13 igenomes config
 - [[#39](https://github.com/nf-core/nascent/issues/39)] - Add PINTS for TSS identification
 - [[#71](https://github.com/nf-core/nascent/issues/71)] - Add FASTP for adapter trimming
 - [[#77](https://github.com/nf-core/nascent/issues/77)] - Add dedup subworkflow

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,9 +1,9 @@
 report_comment: >
-  
+
   This report has been generated by the <a href="https://github.com/nf-core/nascent/releases/tag/2.1.1" target="_blank">nf-core/nascent</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/nascent/2.1.1/docs/output" target="_blank">documentation</a>.
-  
+
 report_section_order:
   "nf-core-nascent-methods-description":
     order: -1000

diff --git a/modules.json b/modules.json
@@ -38,7 +38,7 @@
                     "bwa/mem": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_bwa", "modules"]
                     },
                     "bwamem2/index": {
                         "branch": "master",
@@ -98,7 +98,7 @@
                     },
                     "gffread": {
                         "branch": "master",
-                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
@@ -108,27 +108,27 @@
                     },
                     "homer/findpeaks": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["homer/groseq"]
                     },
                     "homer/maketagdirectory": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["homer/groseq"]
                     },
                     "homer/makeucscfile": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["homer/groseq"]
                     },
                     "homer/pos2bed": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["homer/groseq"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "pints/caller": {
@@ -168,27 +168,27 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["bam_sort_stats_samtools", "bam_dedup_stats_samtools_umitools"]
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+                        "installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "subread/featurecounts": {
@@ -198,7 +198,7 @@
                     },
                     "umitools/dedup": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
                         "installed_by": ["bam_dedup_stats_samtools_umitools"]
                     },
                     "untar": {
@@ -212,22 +212,27 @@
                 "nf-core": {
                     "bam_dedup_stats_samtools_umitools": {
                         "branch": "master",
-                        "git_sha": "41891ec2c3704911cd68b9317f26545b95a1c48d",
+                        "git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "3911652a6b24249358f79e8b8466338d63efb2a2",
-                        "installed_by": ["subworkflows"]
+                        "git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
+                        "installed_by": ["fastq_align_bwa", "subworkflows"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "92eb5091ae5368a60cda58b3a0ced8b36d715b0f",
-                        "installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools"]
+                        "git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
+                        "installed_by": ["bam_dedup_stats_samtools_umitools", "bam_sort_stats_samtools", "subworkflows"]
+                    },
+                    "fastq_align_bwa": {
+                        "branch": "master",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "installed_by": ["subworkflows"]
                     },
                     "homer/groseq": {
                         "branch": "master",
-                        "git_sha": "07c9080d7b66a325e8e67d9c57e10083ca8b9db4",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml
diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf
diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml
diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test
diff --git a/modules/nf-core/gffread/tests/main.nf.test.snap b/modules/nf-core/gffread/tests/main.nf.test.snap
diff --git a/modules/nf-core/gffread/tests/nextflow.config b/modules/nf-core/gffread/tests/nextflow.config
diff --git a/modules/nf-core/gffread/tests/tags.yml b/modules/nf-core/gffread/tests/tags.yml
diff --git a/modules/nf-core/homer/findpeaks/environment.yml b/modules/nf-core/homer/findpeaks/environment.yml
diff --git a/modules/nf-core/homer/findpeaks/main.nf b/modules/nf-core/homer/findpeaks/main.nf
diff --git a/modules/nf-core/homer/findpeaks/meta.yml b/modules/nf-core/homer/findpeaks/meta.yml