From 542f822ca68c9d9835e50092096150c7f97b73ab Mon Sep 17 00:00:00 2001
From: Sam Nicholls <sam.nicholls@nanoporetech.com>
Date: Tue, 4 Jul 2023 10:13:05 +0000
Subject: [PATCH] Reconcile template

---
 .gitlab-ci.yml    | 12 ++++++------
 lib/CWUtil.groovy | 26 ++++++++++++++++++++++++++
 nextflow.config   | 12 ++++++------
 3 files changed, 38 insertions(+), 12 deletions(-)
 create mode 100644 lib/CWUtil.groovy

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a7b7c80..33bb5a3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -77,7 +77,7 @@ docker-run:
                   --de_analysis \
                   --ref_genome differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \
                 --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
-                --direct_rna --minimap_index_opts \\-k15"
+                --direct_rna --minimap_index_opts '-k 15'"
               NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
         - if: $MATRIX_NAME == "only_differential_expression"
           variables:
@@ -87,7 +87,7 @@ docker-run:
                   --de_analysis \
                   --ref_genome differential_expression/hg38_chr20.fa \
                 --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \
-                --direct_rna --minimap_index_opts \\-k15 \
+                --direct_rna --minimap_index_opts '-k 15' \
                 --ref_transcriptome differential_expression/ref_transcriptome.fasta \
                 --transcriptome_assembly false"
               NF_IGNORE_PROCESSES: >
@@ -101,7 +101,7 @@ docker-run:
                   --de_analysis \
                   --ref_genome differential_expression/hg38_chr20.fa \
                 --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \
-                --direct_rna --minimap_index_opts \\-k15 \
+                --direct_rna --minimap_index_opts '-k 15' \
                 --ref_transcriptome differential_expression/ref_transcriptome.fasta \
                 --transcriptome_assembly false"
               NF_IGNORE_PROCESSES: >
@@ -110,14 +110,14 @@ docker-run:
         - if: $MATRIX_NAME == "ncbi_gzip"
           variables:
               NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
-              NF_WORKFLOW_OPTS: "-executor.$$local.memory 16GB \
+              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
 --fastq  differential_expression/differential_expression_fastq \
                   --transcriptome-source precomputed \
                   --de_analysis \
                   --ref_genome differential_expression/GRCh38.p14.NCBI_test.fna.gz \
                 --ref_annotation differential_expression/GRCh38.p14_NCBI_test.gtf.gz \
-                --direct_rna --minimap_index_opts \\-w25 \
+                --direct_rna --minimap_index_opts '-w 25' \
                --transcriptome_assembly false"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,merge_transcriptomes,assemble_transcripts,
-                build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam           
\ No newline at end of file
+                build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam           
diff --git a/lib/CWUtil.groovy b/lib/CWUtil.groovy
new file mode 100644
index 0000000..8a73759
--- /dev/null
+++ b/lib/CWUtil.groovy
@@ -0,0 +1,26 @@
+/* Miscellaneous utilities for workflows from the ONT Customer Workflows Group.
+ */
+class CWUtil {
+
+    /* Mutate the global Nextflow params map
+    *
+    * Occasionally, we may wish to mutate the value of a parameter provided
+    * by the user. Typically, this leads to workflows with `params.my_param`
+    * and `params._my_param` which is ripe for confusion. Instead, we can
+    * mutate the parameter value in the Nextflow params ScriptMap itself
+    * with the following call:
+    *
+    *     CWUtil.mutateParam(params, k, v)
+    *
+    * This is possible as Groovy actually has a surprisingly loose
+    * definition of "private", and allows us to call the private `allowNames`
+    * method on the ScriptMap which removes the read-only status for a key set.
+    * We can follow this up with a call to the private `put0` to reinsert
+    * the key and mark it as read-only again.
+    */
+    public static void mutateParam(nf_params, key, value) {
+        Set s = [key] // must be a set to allow call to allowNames
+        nf_params.allowNames(s)
+        nf_params.put0(key, value)
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index 6dc6b57..e3d10aa 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -97,12 +97,12 @@ params {
 
     wf {
       example_cmd = [
-          "--fastq test_data/fastq",
-          "--ref_genome test_data/SIRV_150601a.fasta",
-          "--ref_annotation test_data/SIRV_isofroms.gtf",
-          "--jaffal_refBase chr20/",
-          "--jaffal_genome hg38",
-          "--jaffal_annotation genCode22"
+          "--condition_sheet 'wf-transcriptomes-demo/condition_sheet.tsv'",
+          "--direct_rna",
+          "--fastq 'wf-transcriptomes-demo/differential_expression_fastq'",
+          "--minimap_index_opts '-k15'",
+          "--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'",
+          "--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'",
       ]
     agent = null
     container_sha = "sha203915eb4b4dd444cb2e845d0b9f7814e26b7b5c"