Merge pull request #51 from bedapub/report

removed ml
bedapub · Feb 7, 2024 · f07fb4c · f07fb4c
2 parents 45b85a7 + d38a586
commit f07fb4c
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diff --git a/splicekit/core/anchors.py b/splicekit/core/anchors.py
@@ -81,7 +81,6 @@ def write_jobs_featureCounts(library_type='single-end', library_strand='NONE'):
 #SBATCH --output={logs_dir}/{anchor_type}_anchors_{sample_id}.out # Output file
 #SBATCH --error={logs_dir}/{anchor_type}_anchors_{sample_id}.err  # Error file
 
-module load Subread/2.0.3-GCC-9.3.0
 {container} featureCounts {library_type_insert}-s {library_strand_insert} -M -O -T 12 -F GTF -f -t anchor -g {anchor_type}_anchor_id -a {gtf_fname} -o {out_fname} {sam_fname} 
 # featureCount outputs command as first line of file, get rid of this first line and replace header for further parsing
 # next, we are only interested in the 1st and 7th column (anchor_id and count)
@@ -105,8 +104,6 @@ def write_jobs_featureCounts(library_type='single-end', library_strand='NONE'):
 #BSUB -o {logs_dir}/{anchor_type}_anchors_{sample_id}.out # Output file
 #BSUB -e {logs_dir}/{anchor_type}_anchors_{sample_id}.err # Error file    
     
-ml .testing
-ml Subread/2.0.3-GCC-9.3.0
 {container} featureCounts {library_type_insert}-s {library_strand_insert} -M -O -T 12 -F GTF -f -t anchor -g {anchor_type}_anchor_id -a {gtf_fname} -o {out_fname} {sam_fname} 
 # featureCount outputs command as first line of file, get rid of this first line and replace header for further parsing
 # next, we are only interested in the 1st and 7th column (anchor_id and count)

diff --git a/splicekit/core/exons.py b/splicekit/core/exons.py
@@ -85,7 +85,6 @@ def write_jobs_featureCounts(library_type='single-end', library_strand='NONE'):
 #SBATCH --output={logs_dir}/exons_{sample_id}.out     # Output file
 #SBATCH --error={logs_dir}/exons_{sample_id}.err      # Error file
     
-module load Subread/2.0.3-GCC-9.3.0
 {container} featureCounts {library_type_insert}-s {library_strand_insert} -M -O -T 12 -F GTF -f -t exon -g exon_id -a {gtf_fname} -o {out_fname} {sam_fname} 
 # featureCount outputs command as first line of file, get rid of this first line and replace header for further parsing
 # next, we are only interested in the 1st and 7th column (exon_id and count)
@@ -110,8 +109,6 @@ def write_jobs_featureCounts(library_type='single-end', library_strand='NONE'):
 #BSUB -o {logs_dir}/exons_{sample_id}.out # Output file
 #BSUB -e {logs_dir}/exons_{sample_id}.err # Error file    
     
-ml .testing
-ml Subread/2.0.3-GCC-9.3.0
 {container} featureCounts {library_type_insert}-s {library_strand_insert} -M -O -T 12 -F GTF -f -t exon -g exon_id -a {gtf_fname} -o {out_fname} {sam_fname} 
 # featureCount outputs command as first line of file, get rid of this first line and replace header for further parsing
 # next, we are only interested in the 1st and 7th column (exon_id and count)

diff --git a/splicekit/core/genes.py b/splicekit/core/genes.py
@@ -85,8 +85,6 @@ def write_jobs_featureCounts(library_type='single-end', library_strand='NONE'):
 #SBATCH --output={logs_dir}/genes_{sample_id}.out     # Output file
 #SBATCH --error={logs_dir}/genes_{sample_id}.err      # Error file    
             
-
-module load Subread/2.0.3-GCC-9.3.0
 {container} featureCounts {library_type_insert}-s {library_strand_insert} -M -O -T 12 -F GTF -f -t exon -g gene_id -a {gtf_fname} -o {out_fname} {sam_fname} 
 # featureCount outputs command as first line of file, get rid of this first line and replace header for further parsing
 # next, we are only interested in the 1st and 7th column (gene_id and count)
@@ -111,8 +109,6 @@ def write_jobs_featureCounts(library_type='single-end', library_strand='NONE'):
 #BSUB -o {logs_dir}/genes_{sample_id}.out   # Output file
 #BSUB -e {logs_dir}/genes_{sample_id}.err   # Error file    
     
-ml .testing
-ml Subread/2.0.3-GCC-9.3.0
 {container} featureCounts {library_type_insert}-s {library_strand_insert} -M -O -T 12 -F GTF -f -t exon -g gene_id -a {gtf_fname} -o {out_fname} {sam_fname} 
 # featureCount outputs command as first line of file, get rid of this first line and replace header for further parsing
 # next, we are only interested in the 1st and 7th column (gene_id and count)