Fix for issue #201

nf-core · Oct 27, 2022 · 021dcb2 · 021dcb2
1 parent 91d00dc
commit 021dcb2
Show file tree

Hide file tree

Showing 8 changed files with 27 additions and 27 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Dev
 
+* Updated FASTP module to allow direct addition of adapter_fasta file to it
+
 ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
 
 ### Enhancements & fixes

diff --git a/conf/modules.config b/conf/modules.config
@@ -105,7 +105,6 @@ if (!params.skip_fastp) {
             params.fastp_min_length > 0    ? "-l ${params.fastp_min_length}" : "",
             params.fastp_max_length > 0    ? "--max_len1 ${params.fastp_max_length}" : "",
             params.three_prime_adapter == null ?  '' : "--adapter_sequence ${params.three_prime_adapter}",
-            params.fastp_known_mirna_adapters == null ? '' : "--adapter_fasta ${params.fastp_known_mirna_adapters}"
         ].join(" ").trim()
             publishDir = [
                 [

diff --git a/modules.json b/modules.json
@@ -15,11 +15,11 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "f6a11408536fbee6cbea1f5977605011873de3ca"
                     },
                     "multiqc": {
                         "branch": "master",

diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/subworkflows/nf-core/fastqc_fastp.nf b/subworkflows/nf-core/fastqc_fastp.nf
diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf
@@ -38,6 +38,7 @@ ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config
 ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
 ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
 ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
+ch_fastp_adapters          = Channel.fromPath(params.fastp_known_mirna_adapters, checkIfExists: true)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -126,6 +127,7 @@ workflow SMRNASEQ {
 
     FASTQC_FASTP (
         ch_cat_fastq,
+        ch_fastp_adapters,
         false,
         false
     )
-Original file line number
+Diff line change
@@ Expand Up @@
     ## Dev
+    * Updated FASTP module to allow direct addition of adapter_fasta file to it
     ## [v2.1.0](https://github.com/nf-core/smrnaseq/releases/tag/2.1.0) - 2022-10-20 Maroon Tin Dalmatian
     ### Enhancements & fixes
@@ Expand Down @@