Merge pull request #85 from sanger-bentley-group/dev

Dev
sanger-bentley-group · Mar 24, 2023 · ed997ea · ed997ea
2 parents e63991a + 8e3ba5e
commit ed997ea
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 13 deletions.
diff --git a/README.md b/README.md
@@ -36,7 +36,11 @@ GBS Typer relies on Nextflow and Docker.
 Download:
 1. [Docker](https://www.docker.com/).
 2. [Nextflow](https://www.nextflow.io/).
-3. Clone repository:
+3. Move `nextflow` to your PATH
+```
+mv nextflow /usr/local/bin/
+```
+4. Clone repository:
 ```
 git clone https://github.com/sanger-pathogens/GBS-Typer-sanger-nf.git
 cd GBS-Typer-sanger-nf

diff --git a/modules/res_alignments.nf b/modules/res_alignments.nf
@@ -17,18 +17,6 @@ process srst2_for_res_typing {
     srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id} --log --save_scores --min_coverage ${min_coverage} --max_divergence ${max_divergence} --gene_db ${db}
 
     touch ${pair_id}__fullgenes__${db_name}__results.txt
-
-    # Clean directory
-    mkdir output
-    mv ${pair_id}*.bam output
-    mv ${pair_id}__fullgenes__${db_name}__results.txt output
-    find . -maxdepth 1 -type f -delete
-    unlink ${reads[0]}
-    unlink ${reads[1]}
-    unlink ${db}
-    mv output/${pair_id}*.bam .
-    mv output/${pair_id}__fullgenes__${db_name}__results.txt .
-    rm -d output
     """
 }