updated run instructions

iraiosub · Dec 13, 2023 · 167fec5 · 167fec5
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diff --git a/README.md b/README.md
@@ -49,21 +49,21 @@ We recommend using Nextflow with `Java 17.0.9` or later.
 2. Pull the desired version of the pipeline from the GitHub repository:
 
 ```
-nextflow pull iraiosub/riboseq-flow -r v1.0.0
+nextflow pull iraiosub/riboseq-flow -r v1.0.1
 ```
 
 3. Run the pipeline on the provided test dataset:
 
 Using Singularity:
 
 ```
-nextflow run iraiosub/riboseq-flow -r v1.0.0 -profile test,singularity
+nextflow run iraiosub/riboseq-flow -r v1.0.1 -profile test,singularity
 ```
 
 or using Docker:
 
 ```
-nextflow run iraiosub/riboseq-flow -r v1.0.0 -profile test,docker
+nextflow run iraiosub/riboseq-flow -r v1.0.1 -profile test,docker
 ```
 
 4. Check succesful execution.
@@ -75,7 +75,7 @@ nextflow run iraiosub/riboseq-flow -r v1.0.0 -profile test,docker
 2. Pull the desired version of the pipeline from the GitHub repository:
 
 ```
-nextflow pull iraiosub/riboseq-flow -r v1.0.0
+nextflow pull iraiosub/riboseq-flow -r v1.0.1
 ```
 
 3. Create a samplesheet `samplesheet.csv` with information about the samples you would like to analyse before running the pipeline. It has to be a comma-separated file with 2 columns, and a header row as shown in the example below. 

diff --git a/modules/local/ribowaltz.nf b/modules/local/ribowaltz.nf
@@ -66,7 +66,7 @@ process GET_PSITE_TRACKS {
     path(fai)
 
     output:
-    path("*.psites.bed"), emit: psite_bed
+    path("*.psites.bed.gz"), emit: psite_bed
     // path("*.bigwig"), emit: psite_bigwig
 
     script:

diff --git a/run.sh b/run.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/sh
-#SBATCH --job-name=nf-ribo-seq-test
+#SBATCH --job-name=riboseq-flow-test
 #SBATCH --ntasks=1
 #SBATCH --time=24:00:00
 #SBATCH --mem-per-cpu=4G
@@ -17,7 +17,7 @@ ml Singularity/3.6.4
 export NXF_SINGULARITY_CACHEDIR=/nemo/lab/ulej/home/shared/singularity
 export NXF_HOME=/nemo/lab/ulej/home/users/luscomben/users/iosubi/.nextflow
 
-nextflow pull iraiosub/riboseq-flow -r main
+nextflow pull iraiosub/riboseq-flow -r v1.0.1
 
-nextflow run iraiosub/riboseq-flow -r main \
+nextflow run iraiosub/riboseq-flow -r v1.0.1 \
 -profile test,singularity