Merge branch 'remove_transcriptoe_assembly_option' into 'dev'

Remove unused parameter

See merge request epi2melabs/workflows/wf-transcriptomes!116

Author: sarahjeeeze

.gitlab-ci.yml

@@ -89,7 +89,7 @@ docker-run:
                 --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \
                 --direct_rna --minimap_index_opts '-k 15' \
                 --ref_transcriptome differential_expression/ref_transcriptome.fasta \
-                --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
+                --sample_sheet test_data/sample_sheet.csv"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
@@ -103,7 +103,7 @@ docker-run:
                 --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \
                 --direct_rna --minimap_index_opts '-k 15' \
                 --ref_transcriptome differential_expression/ref_transcriptome.fasta \
-                --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
+                --sample_sheet test_data/sample_sheet.csv"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
@@ -117,7 +117,7 @@ docker-run:
                   --ref_genome differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \
                 --ref_annotation differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
                 --direct_rna --minimap_index_opts '-w 25' \
-               --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
+               --sample_sheet test_data/sample_sheet.csv"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,merge_transcriptomes,assemble_transcripts,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam           

README.md

@@ -241,7 +241,8 @@ nextflow run epi2me-labs/wf-transcriptomes \
   --de_analysis \
   --ref_genome differential_expression/hg38_chr20.fa \
   --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
-  --direct_rna --minimap_index_opts \-k15
+  --direct_rna --minimap_index_opts \
+  -k15
 ```
 You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
 eg.
@@ -251,9 +252,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
   --de_analysis \
   --ref_genome differential_expression/hg38_chr20.fa \
   --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
-  --direct_rna --minimap_index_opts \-k15 \
-  --ref_transcriptome differential_expression/ref_transcriptome.fasta \
-  --transcriptome_assembly false
+  --direct_rna --minimap_index_opts \
+  -k15 \
+  --ref_transcriptome differential_expression/ref_transcriptome.fasta
 ```
 
 ## Workflow outputs

docs/quickstart.md

@@ -151,7 +151,8 @@ nextflow run epi2me-labs/wf-transcriptomes \
   --de_analysis \
   --ref_genome differential_expression/hg38_chr20.fa \
   --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
-  --direct_rna --minimap_index_opts \-k15
+  --direct_rna --minimap_index_opts \
+  -k15
 ```
 You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
 eg.
@@ -161,9 +162,9 @@ nextflow run epi2me-labs/wf-transcriptomes \
   --de_analysis \
   --ref_genome differential_expression/hg38_chr20.fa \
   --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
-  --direct_rna --minimap_index_opts \-k15 \
-  --ref_transcriptome differential_expression/ref_transcriptome.fasta \
-  --transcriptome_assembly false
+  --direct_rna --minimap_index_opts \
+  -k15 \
+  --ref_transcriptome differential_expression/ref_transcriptome.fasta
 ```
 
 ## Workflow outputs