Fix Salmon index for Refseq build

Author: guillaumecharbonnier

src/python/tidy_samples_by_metadata.py

@@ -127,6 +127,9 @@ def tidy_samples(
     # df = df.dropna(subset = "sample_name")
     samples.fillna("NA", inplace=True)
 
+    # Remove the '.0' suffix from the 'run' column
+    samples['run'] = samples['run'].astype(str).str.replace('.0', '', regex=False)
+
     # Iterate over by_merge_metadata to create the merged columns if not None
     if by_merge_metadata is not None:
         for merge_metadata in by_merge_metadata:

src/snakemake/rules/danpos_wiq.smk

@@ -31,8 +31,8 @@ rule danpos_wiq:
     conda:
         "../envs/danpos.yaml"
     wildcard_constraints:
-        wig_to_wiq = "[a-zA-Z0-9_-]+",
-        reference = "[a-zA-Z0-9_-]+"
+        wig_to_wiq = "[a-zA-Z0-9_+-]+",
+        reference = "[a-zA-Z0-9_+-]+"
     threads:
         1
     priority:

src/snakemake/rules/salmon_index.smk

@@ -24,16 +24,18 @@ rule salmon_index_refseq_with_decoys:
         rna = expand(
             "out/wget/https/ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.{number}.rna.fna.gz",
             number=range(1, 17)  # Specify the range of numbers from 1 to 16
-        )
+        ),
         dna = "out/wget/ftp/ftp.ensembl.org/pub/release-102/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"
     output:
         directory("out/salmon/index_refseq_with_decoys/homo_sapiens")
+    conda:
+        "../envs/salmon.yaml"
     shell:
         """
         mkdir -p {output}
         cat {input} > {output}/transcriptome_genome.fa.gz
 
-        zcat {input.dna} | grep "^>" | cut -d " " -f 1 | sed "s/>//g" > {output}/decoys.txt
+        zgrep "^>" {input.dna} | cut -d " " -f 1 | sed "s/>//g" > {output}/decoys.txt
 
         salmon index -t {output}/transcriptome_genome.fa.gz -d {output}/decoys.txt -i {output}
 

src/snakemake/tables/salmon_index_ids.tsv

@@ -1,5 +1,6 @@
 id	path
 salmon-index-GRCh38-ensembl-r103-cdna	"out/salmon/index/wget/http/ftp.ensembl.org/pub/release-103/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all"
+salmon-index-GRCh38-RefSeq	"out/salmon/index_refseq_with_decoys/homo_sapiens"
 salmon-index-GRCh38-ensembl-r103	"out/salmon/index_ensembl_with_decoys/release-103/fasta/homo_sapiens/Homo_sapiens.GRCh38"
 salmon-index-GRCh38-ensembl-r102	"out/salmon/index_ensembl_with_decoys/release-102/fasta/homo_sapiens/Homo_sapiens.GRCh38"
 salmon-index-GRCm38-ensembl-r102	"out/salmon/index_ensembl_with_decoys/release-102/fasta/mus_musculus/Mus_musculus.GRCm38"