feat: Salmon-tximport meta-wrapper pathvars update

meta/bio/salmon_tximport/meta.yaml

@@ -18,3 +18,16 @@ description: >
     +----------------+----------+------------------------------------------------+
 authors:
   - Thibault Dayris
+pathvars:
+  default:
+    - results
+    - resources
+    - logs
+  custom:
+    transcriptome_sequence: Path to FASTA file with transcriptome sequence
+    genome_sequence: Path to FASTA file with genome sequence
+    genome_annotation: Path to GTF file with genome annotation
+    reads_r1: Path/pattern for FASTQ files with R1 reads
+    reads_r2: Path/pattern for FASTQ files with R2 reads
+    tx_to_gene: Path to TSV table with transcript_id <tab> gene_id
+    per: Pattern for sample identifiers, e.g. ``"{sample}"``

meta/bio/salmon_tximport/meta_wrapper.smk

@@ -1,24 +1,24 @@
 rule salmon_decoy_sequences:
     input:
-        transcriptome="resources/transcriptome.fasta",
-        genome="resources/genome.fasta",
+        transcriptome="<transcriptome_sequence>",
+        genome="<genome_sequence>",
     output:
-        gentrome=temp("resources/gentrome.fasta"),
-        decoys=temp("resources/decoys.txt"),
+        gentrome=temp("<resources>/gentrome.fasta"),
+        decoys=temp("<resources>/decoys.txt"),
     threads: 1
     log:
-        "decoys.log",
+        "<logs>/decoys.log",
     wrapper:
         "v6.0.0/bio/salmon/decoys"
 
 
 rule salmon_index_gentrome:
     input:
-        sequences="resources/gentrome.fasta",
-        decoys="resources/decoys.txt",
+        sequences="<resources>/gentrome.fasta",
+        decoys="<resources>/decoys.txt",
     output:
         multiext(
-            "salmon/transcriptome_index/",
+            "<resources>/salmon_gentrome_index/",
             "complete_ref_lens.bin",
             "ctable.bin",
             "ctg_offsets.bin",
@@ -37,7 +37,7 @@ rule salmon_index_gentrome:
         ),
     cache: True
     log:
-        "logs/salmon/transcriptome_index.log",
+        "<logs>/salmon/gentrome_index.log",
     threads: 2
     params:
         # optional parameters
@@ -48,9 +48,10 @@ rule salmon_index_gentrome:
 
 rule salmon_quant_reads:
     input:
-        r="reads/{sample}.fastq.gz",
+        r1="<reads_r1>",
+        r2="<reads_r2>",
         index=multiext(
-            "salmon/transcriptome_index/",
+            "<resources>/salmon_gentrome_index/",
             "complete_ref_lens.bin",
             "ctable.bin",
             "ctg_offsets.bin",
@@ -67,17 +68,17 @@ rule salmon_quant_reads:
             "seq.bin",
             "versionInfo.json",
         ),
-        gtf="resources/annotation.gtf",
+        gtf="<genome_annotation>",
     output:
-        quant=temp("pseudo_mapping/{sample}/quant.sf"),
-        quant_gene=temp("pseudo_mapping/{sample}/quant.genes.sf"),
-        lib=temp("pseudo_mapping/{sample}/lib_format_counts.json"),
-        aux_info=temp(directory("pseudo_mapping/{sample}/aux_info")),
-        cmd_info=temp("pseudo_mapping/{sample}/cmd_info.json"),
-        libparams=temp(directory("pseudo_mapping/{sample}/libParams")),
-        logs=temp(directory("pseudo_mapping/{sample}/logs")),
+        quant=temp("<results>/pseudo_mapping/<per>/quant.sf"),
+        quant_gene=temp("<results>/pseudo_mapping/<per>/quant.genes.sf"),
+        lib=temp("<results>/pseudo_mapping/<per>/lib_format_counts.json"),
+        aux_info=temp(directory("<results>/pseudo_mapping/<per>/aux_info")),
+        cmd_info=temp("<results>/pseudo_mapping/<per>/cmd_info.json"),
+        libparams=temp(directory("<results>/pseudo_mapping/<per>/libParams")),
+        logs=temp(directory("<results>/pseudo_mapping/<per>/logs")),
     log:
-        "logs/salmon/{sample}.log",
+        "<logs>/salmon/<per>.log",
     params:
         # optional parameters
         libtype="A",
@@ -90,28 +91,35 @@ rule salmon_quant_reads:
 rule tximport:
     input:
         quant=expand(
-            "pseudo_mapping/{sample}/quant.sf", sample=["S1", "S2", "S3", "S4"]
+            "<results>/pseudo_mapping/{sample}/quant.sf",
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         lib=expand(
-            "pseudo_mapping/{sample}/lib_format_counts.json",
-            sample=["S1", "S2", "S3", "S4"],
+            "<results>/pseudo_mapping/{sample}/lib_format_counts.json",
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         aux_info=expand(
-            "pseudo_mapping/{sample}/aux_info", sample=["S1", "S2", "S3", "S4"]
+            "<results>/pseudo_mapping/{sample}/aux_info",
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         cmd_info=expand(
-            "pseudo_mapping/{sample}/cmd_info.json", sample=["S1", "S2", "S3", "S4"]
+            "<results>/pseudo_mapping/{sample}/cmd_info.json",
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         libparams=expand(
-            "pseudo_mapping/{sample}/libParams", sample=["S1", "S2", "S3", "S4"]
+            "<results>/pseudo_mapping/{sample}/libParams",
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
-        logs=expand("pseudo_mapping/{sample}/logs", sample=["S1", "S2", "S3", "S4"]),
-        tx_to_gene="resources/tx2gene.tsv",
+        logs=expand(
+            "<results>/pseudo_mapping/{sample}/logs",
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
+        ),
+        tx_to_gene="<tx_to_gene>",
     output:
-        txi="tximport/SummarizedExperimentObject.RDS",
+        txi="<results>/tximport/SummarizedExperimentObject.RDS",
     params:
         extra="type='salmon'",
     log:
-        "logs/tximport.log"
+        "<logs>/tximport.log",
     wrapper:
         "v6.0.2/bio/tximport"

meta/bio/salmon_tximport/test/Snakefile

@@ -2,7 +2,15 @@ from snakemake.utils import min_version
 
 min_version("9.13.1")
 
+
+configfile: "config.yaml"
+
+
 module salmon_tximport:
-    meta_wrapper: "file:.."
+    meta_wrapper:
+        "file:.."
+    config:
+        config
+
 
-use rule * from salmon_tximport
+use rule * from salmon_tximport

meta/bio/salmon_tximport/test/config.yaml

@@ -0,0 +1,14 @@
+pathvars:
+  transcriptome_sequence: "resources/transcriptome.fasta"
+  genome_sequence: "resources/genome.fasta"
+  genome_annotation: "resources/annotation.gtf"
+  tx_to_gene: "resources/tx2gene.tsv"
+  per: "{sample}"
+  reads_r1: "reads/{sample}_R1.fq.gz"
+  reads_r2: "reads/{sample}_R2.fq.gz"
+  resources: "resources"
+
+salmon_tximport_submodule:
+  samples:
+    - "S1"
+    - "S2"

meta/bio/salmon_tximport/test/resources/genome.fasta.fai

@@ -0,0 +1 @@
+chromosome1	927	13	79	80

meta/bio/salmon_tximport/test/resources/transcriptome.fasta

@@ -1,4 +1,5 @@
 >transcript1
-CCAGGCTCGTATGTACATCGCTCCTCAAAGTGAGGGGAAGTCCTAAT
+CAGGCTCGTATGTACATCGCTCCTCAAAGTGAGGGGAAGTCCTAATCGG
 >transcript2
-CATCTCCCTGAGTCGGTTTAAAGATTGTCTTGTATGCGTACTCTTGATAGGTAACCCG
+CAGGCTCGTATGTACATCGCTCCTCAAAGTGAGGGGAAGTCCTAATCGGATACCGATTGGACTCTTGAGT
+ACCGGCCCTGT

meta/bio/salmon_tximport/test/resources/transcriptome.fasta.fai

@@ -0,0 +1,2 @@
+transcript1	49	13	49	50
+transcript2	81	76	70	71

test_wrappers.py

@@ -1138,7 +1138,7 @@ def test_salmon_tximport_meta(run):
             "--cores",
             "2",
             "--use-conda",
-            "tximport/SummarizedExperimentObject.RDS",
+            "results/tximport/SummarizedExperimentObject.RDS",
         ],
     )