Merge pull request #149 from jma1991/update-samtools-module

Update samtools module
nf-core · Aug 21, 2024 · 05a0402 · 05a0402
2 parents aab6219 + 698152d
commit 05a0402
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.4 - 2024-04-21
+
+- Fixed incorrect assignment of cluster groups (Issue #131).
+
 ## v1.0.3 - 2024-02-23
 
 - Improved TPM file splitting performance (Issue #120).

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnasplice/releases/tag/1.0.3" target="_blank">nf-core/rnasplice</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnasplice/releases/tag/1.0.4" target="_blank">nf-core/rnasplice</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnasplice/1.0.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnasplice/1.0.4/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-rnasplice-methods-description":

diff --git a/modules.json b/modules.json
@@ -57,13 +57,13 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules", "bam_stats_samtools"]
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules", "bam_stats_samtools"]
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
@@ -77,7 +77,7 @@
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "star/align": {
@@ -131,7 +131,7 @@
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "bedgraph_bedclip_bedgraphtobigwig": {

diff --git a/modules/local/suppa_clusterevents.nf b/modules/local/suppa_clusterevents.nf
@@ -11,7 +11,7 @@ process CLUSTEREVENTS {
     input:
     tuple val(cond1), val(cond2), path(dpsi)
     tuple val(cond1), val(cond2), path(psivec)
-    val group_ranges // e.g. 1-3,4-6
+    tuple val(cond1), val(cond2), val(group_ranges) // e.g. 1-3,4-6
     val prefix
     val clusterevents_dpsithreshold    // val params.clusterevents_dpsithreshold
     val clusterevents_eps              // val params.clusterevents_eps

diff --git a/modules/local/suppa_clustergroups.nf b/modules/local/suppa_clustergroups.nf
@@ -11,7 +11,7 @@ process CLUSTERGROUPS {
     tuple val(cond1), val(cond2), path(psivec)
 
     output:
-    stdout
+    tuple val(cond1), val(cond2), stdout
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.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/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml
diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test