Merge pull request #486 from nf-core/test-replicates

Test replicates
nf-core · Dec 12, 2024 · be9f86a · be9f86a
2 parents e7ea5d3 + ceed526
commit be9f86a
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Showing 37 changed files with 810 additions and 146 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,8 +16,9 @@
 - 🔧 reorg individual configs to `conf/modules/` named configs [#459](https://github.com/nf-core/methylseq/pull/469)
 - 🔧 `run_preseq` param + skip preseq/lcextrap module by default [#458](https://github.com/nf-core/methylseq/pull/470)
 - 🔧 `run_qualimap` param + skip qualimap module by default [#367](https://github.com/nf-core/methylseq/pull/471)
-- 🔧 Raised Nextflow version requirement to `24.10.2`
+- 🔧 Raised Nextflow version requirement to `24.10.2` in CI
 - 🔧 Update the CI for pipeline-level bwameth GPU Tests [#481](https://github.com/nf-core/methylseq/pull/478)
+- 🔧 Update the CI for pipeline-level bwameth GPU Tests [#477](https://github.com/nf-core/methylseq/pull/486)
 
 ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
 

diff --git a/assets/samplesheet_replicates.csv b/assets/samplesheet_replicates.csv
@@ -0,0 +1,5 @@
+sample,fastq_1,fastq_2,genome
+SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
+SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
+SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,
+Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
diff --git a/modules.json b/modules.json
@@ -42,7 +42,7 @@
                     },
                     "bwameth/align": {
                         "branch": "master",
-                        "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9",
+                        "git_sha": "2edb63067971fb906749e96bf22b23a4ec892a62",
                         "installed_by": ["fastq_align_dedup_bwameth", "modules"]
                     },
                     "bwameth/index": {
@@ -82,7 +82,7 @@
                     },
                     "parabricks/fq2bammeth": {
                         "branch": "master",
-                        "git_sha": "3a897454edabb27d21debfec644e40f7bcfa4c43",
+                        "git_sha": "2edb63067971fb906749e96bf22b23a4ec892a62",
                         "installed_by": ["fastq_align_dedup_bwameth"]
                     },
                     "picard/markduplicates": {
@@ -132,7 +132,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6",
+                        "git_sha": "4c2d06a5e79abf08ba7f04c58e39c7dad75f094d",
                         "installed_by": ["modules"]
                     },
                     "untar": {
@@ -166,7 +166,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "9a1e8bb6a5d205cf7807dcefca872a3314b2f3e6",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test
diff --git a/modules/nf-core/parabricks/fq2bammeth/main.nf b/modules/nf-core/parabricks/fq2bammeth/main.nf
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf