From 8cab847b1c1af6c369c870bba0abf1f0006968e5 Mon Sep 17 00:00:00 2001 From: Johnny Lomas Date: Fri, 6 Dec 2024 13:26:29 -0800 Subject: [PATCH] Pasa .ok files --- bin/Snakefile_annotate | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/bin/Snakefile_annotate b/bin/Snakefile_annotate index ddd843c..63967d2 100644 --- a/bin/Snakefile_annotate +++ b/bin/Snakefile_annotate @@ -2236,13 +2236,8 @@ rule pasaPrep: -a \ -o TRANSCRIPT/PASA/evigene.sam - /opt/miniconda3/opt/pasa-2.5.2/misc_utilities/SAM_to_gff3.minimap2_path1only.pl \ - TRANSCRIPT/PASA/evigene.sam > TRANSCRIPT/PASA/evigene.gff + /opt/miniconda3/opt/pasa-2.5.2/misc_utilities/SAM_to_gtf.pl TRANSCRIPT/PASA/evigene.sam > TRANSCRIPT/PASA/evigene.gtf - gffread TRANSCRIPT/PASA/evigene.gff \ - -T -F \ - --keep-exon-attrs \ - -o TRANSCRIPT/PASA/evigene.gtf sed -i 's/\\ .*//g' {input.spades} /opt/miniconda3/opt/pasa-2.5.2/misc_utilities/gff3_file_to_proteins.pl \ @@ -2269,6 +2264,10 @@ rule pasa: shell: """ rm __pasa_pasa.sqlite_SQLite_chkpts/*.ok || echo 'No pasa .ok files to remove... continuing' + rm __all_transcripts.fasta.transdecoder_dir/*/*.ok || echo 'No pasa transdecoder .ok files to remove...continuing' + rm __all_transcripts.fasta.transdecoder_dir.__checkpoints/*.ok || echo 'No checkpoints' + rm __all_transcripts.fasta.transdecoder_dir.__checkpoints_longorfs/*.ok || echo 'No longorfs' + rm minimap2.splice_alignments.gff3.ok spades.okay.tr.clean.mm2.bam.ok transcripts_for_pasa.fasta.clean.mm2.bam.ok || echo 'No files to remove' export TMPDIR=./TMP export SLURM_TMPDIR=./TMP