Merge branch 'dev' into pipeline_level_tests_simple

CHANGELOG.md

@@ -62,6 +62,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1261](https://github.com/nf-core/rnaseq/pull/1261) - Add more tests for PREPARE_GENOME
 - [PR #1265](https://github.com/nf-core/rnaseq/pull/1265) - Small updates noticed during code review
 - [PR #1266](https://github.com/nf-core/rnaseq/pull/1266) - Delete unecessary tags from nf.test files for modules and subworkflows
+- [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
 
 ### Parameters
 

modules.json

@@ -33,7 +33,7 @@
                     "custom/tx2gene": {
                         "branch": "master",
                         "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "dupradar": {
                         "branch": "master",
@@ -88,7 +88,7 @@
                     "kallisto/quant": {
                         "branch": "master",
                         "git_sha": "de5811dd9ca15af1e131806001bcaae909e42021",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "multiqc": {
                         "branch": "master",
@@ -97,7 +97,7 @@
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
+                        "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087",
                         "installed_by": ["bam_markduplicates_picard"]
                     },
                     "preseq/lcextrap": {
@@ -168,7 +168,7 @@
                     "salmon/quant": {
                         "branch": "master",
                         "git_sha": "03a8562231d575c313266c193a980594b941e3ea",
-                        "installed_by": ["fastq_subsample_fq_salmon", "modules"]
+                        "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
@@ -227,7 +227,7 @@
                     "summarizedexperiment/summarizedexperiment": {
                         "branch": "master",
                         "git_sha": "05a252a330273c67795aed2b18e86c53c4c9382a",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "trimgalore": {
                         "branch": "master",
@@ -236,8 +236,8 @@
                     },
                     "tximeta/tximport": {
                         "branch": "master",
-                        "git_sha": "03a8562231d575c313266c193a980594b941e3ea",
-                        "installed_by": ["modules"]
+                        "git_sha": "c275c3baac6df8f0c7c500760a0cf014ce7b525d",
+                        "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "ucsc/bedclip": {
                         "branch": "master",
@@ -280,7 +280,7 @@
                     },
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_rseqc": {
@@ -327,6 +327,11 @@
                         "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
                         "installed_by": ["subworkflows"]
                     },
+                    "quantify_pseudo_alignment": {
+                        "branch": "master",
+                        "git_sha": "bca4985339b3ba879f457565806deb2377873b83",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",