Merge pull request #1036 from drpatelh/updates

Fix #1011
nf-core · May 31, 2023 · e9aff1d · e9aff1d
2 parents 9472aaa + 277bd33
commit e9aff1d
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Showing 25 changed files with 142 additions and 75 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,13 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[#1011](https://github.com/nf-core/rnaseq/issues/1011)] - FastQ files from UMI-tools not being passed to fastp
 - [PR #1016](https://github.com/nf-core/rnaseq/pull/1016) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #1025](https://github.com/nf-core/fetchngs/pull/1025) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
 
 ### Software dependencies
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| `fastp`    | 0.23.2      | 0.23.4      |
 | `samtools` | 1.16.1      | 1.17        |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.

diff --git a/conf/test.config b/conf/test.config
@@ -24,16 +24,16 @@ params {
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv"
 
     // Genome references
-    fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genome.fasta"
-    gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz"
-    gff                = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz"
-    transcript_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta"
-    additional_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz"
-
-    bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt"
-    hisat2_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz"
-    salmon_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz"
-    rsem_index         = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz"
+    fasta              = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genome.fasta"
+    gtf                = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gtf.gz"
+    gff                = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/genes.gff.gz"
+    transcript_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/transcriptome.fasta"
+    additional_fasta   = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/gfp.fa.gz"
+
+    bbsplit_fasta_list = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/bbsplit_fasta_list.txt"
+    hisat2_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/hisat2.tar.gz"
+    salmon_index       = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/salmon.tar.gz"
+    rsem_index         = "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/rsem.tar.gz"
 
     // Other parameters
     skip_bbsplit        = false

diff --git a/conf/test_cache.config b/conf/test_cache.config
@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
+    Nextflow config file for running minimal tests using cached / offline test data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines input files and everything required to run a fast and simple pipeline test.
 

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bbmap/bbsplit": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
@@ -27,8 +27,8 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules", "fastq_fastqc_umitools_fastp"]
+                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
                     "fastqc": {
                         "branch": "master",
@@ -52,22 +52,22 @@
                     },
                     "hisat2/align": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "hisat2/build": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["modules"]
                     },
                     "hisat2/extractsplicesites": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["bam_markduplicates_picard"]
                     },
                     "preseq/lcextrap": {
@@ -166,7 +166,7 @@
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "sortmerna": {
@@ -176,7 +176,7 @@
                     },
                     "star/align": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "57d75dbac06812c59798a48585032f6e50bb1914",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
@@ -230,7 +230,7 @@
                 "nf-core": {
                     "bam_dedup_stats_samtools_umitools": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "e228790f2957152ad2534e39abd7b3878963e89d",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_markduplicates_picard": {
@@ -245,16 +245,16 @@
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": [
+                            "bam_dedup_stats_samtools_umitools",
                             "bam_markduplicates_picard",
-                            "bam_sort_stats_samtools",
-                            "bam_dedup_stats_samtools_umitools"
+                            "bam_sort_stats_samtools"
                         ]
                     },
                     "bedgraph_bedclip_bedgraphtobigwig": {
@@ -269,7 +269,7 @@
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "48dbb403fb2849b3d2c6c2e3eaaedbcca799428d",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {

diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml
diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf
diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml
diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf
diff --git a/modules/nf-core/hisat2/extractsplicesites/meta.yml b/modules/nf-core/hisat2/extractsplicesites/meta.yml
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf