From 167fec50060316fc4cd280d7bc319e14a63bb553 Mon Sep 17 00:00:00 2001
From: Ira Iosub <iosubi@login002.nemo.thecrick.org>
Date: Wed, 13 Dec 2023 20:39:10 +0000
Subject: [PATCH] updated run instructions

---
 README.md                  | 8 ++++----
 modules/local/ribowaltz.nf | 2 +-
 run.sh                     | 6 +++---
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 185f1c0..1783232 100644
--- a/README.md
+++ b/README.md
@@ -49,7 +49,7 @@ 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:
@@ -57,13 +57,13 @@ nextflow pull iraiosub/riboseq-flow -r v1.0.0
 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
index a4d071e..5c2ff64 100644
--- 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
index e899d44..23b0926 100755
--- 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
\ No newline at end of file