Merge pull request #217 from danilodileo/update-full-test

Update full test + modules update
nf-core · Dec 5, 2023 · 163312a · 163312a
2 parents 60d7f58 + 5ba8454
commit 163312a
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Showing 26 changed files with 821 additions and 17 deletions.
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -21,9 +21,9 @@ params {
     genome = 'R64-1-1'
 
     // parameters
-    //skip_eukulele   = false
+    skip_eukulele   = false
     skip_eggnog     = false
     skip_kofamscan  = true
-    //eukulele_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/gtdb_eukulele/'
+    eukulele_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/gtdb_eukulele/'
     eggnog_dbpath   = 's3://ngi-igenomes/test-data/metatdenovo/eggnog/'
 }
diff --git a/modules.json b/modules.json
@@ -37,12 +37,12 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "3e8b0c1144ccf60b7848efbdc2be285ff20b49ee",
                         "installed_by": ["modules"]
                     },
                     "hmmer/hmmsearch": {
@@ -52,7 +52,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
@@ -67,17 +67,17 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
@@ -107,7 +107,7 @@
                     },
                     "subread/featurecounts": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d062b356938ea98d29b298691adf0620d3c3bdf0",
                         "installed_by": ["modules"]
                     },
                     "transdecoder/longorf": {
@@ -136,7 +136,7 @@
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "0da36ce43056d68253d3c422c7137223ac6d3c3a",
                         "installed_by": ["bam_sort_stats_samtools"]
                     }
                 }

diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml
diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test
diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml
diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config