Merge pull request #14 from nf-core/dev

Release 1.1.4
nf-core · Mar 13, 2023 · 977b9bb · 977b9bb
2 parents 26153d7 + 3ccf5f8
commit 977b9bb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,19 @@
 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).
 
+## v1.1.4 - Teal Albatross [13/03/2023]
+
+### `Added`
+
+### `Fixed`
+
+- Update minimap2 path test: Don't set gtf option. It is not expected to be used with minimap2 is chosen.
+- FIX: Don't prepare gtf channel when minimap2 is chosen.
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.1.3 - Blue Grouse [06/03/2023]
 
 ### `Added`

diff --git a/conf/test_minimap2.config b/conf/test_minimap2.config
@@ -23,7 +23,6 @@ params {
     input           = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/samplesheet.csv'
     primers         = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/testdata/primers.fasta'
     fasta           = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.dna.chromosome.19.fasta'
-    gtf             = 'https://raw.githubusercontent.com/nf-core/test-datasets/isoseq/reference/Homo_sapiens.GRCh38.104.chr.13_18_19.gtf'
     rq              = 0.9
     chunk           = 5
     five_prime      = 100

diff --git a/workflows/isoseq.nf b/workflows/isoseq.nf
@@ -93,12 +93,13 @@ workflow ISOSEQ {
     //
     INPUT_CHECK(file(params.input), params.chunk) // Check samplesheet input for PBCCS module
     ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
-
-    SET_CHUNK_NUM_CHANNEL(params.input, params.chunk) // Prepare channels for:
+                                                      // Prepare channels for:
+    SET_CHUNK_NUM_CHANNEL(params.input, params.chunk) // - PBCCS parallelization
     SET_FASTA_CHANNEL(params.fasta)                   // - genome fasta
-    SET_GTF_CHANNEL(params.gtf)                       // - primers fasta
-    SET_PRIMERS_CHANNEL(params.primers)               // - genome gtf
-                                                      // - PBCCS parallelization
+    SET_PRIMERS_CHANNEL(params.primers)               // - primers fasta
+    if (params.aligner == "ultra") {
+        SET_GTF_CHANNEL(params.gtf)                   // - genome gtf
+    }
 
     PBCCS(INPUT_CHECK.out.reads, SET_CHUNK_NUM_CHANNEL.out.chunk_num, params.chunk) // Generate CCS from raw reads
     PBCCS.out.bam // Update meta: update id (+chunkX) and store former id