From b679f61376ab1ecea7cf98b0a833b5ef0d358de2 Mon Sep 17 00:00:00 2001
From: tdayris <thibault.dayris@gustaveroussy.fr>
Date: Mon, 20 Oct 2025 18:06:31 +0200
Subject: [PATCH 1/3] Pathvars attempt

---
 meta/bio/salmon_tximport/meta.yaml            |  13 ++++
 meta/bio/salmon_tximport/meta_wrapper.smk     |  68 ++++++++++--------
 meta/bio/salmon_tximport/test/Snakefile       |  12 +++-
 meta/bio/salmon_tximport/test/config.yaml     |   9 +++
 .../salmon_tximport/test/reads/S1.fastq.gz    | Bin 1198 -> 0 bytes
 .../salmon_tximport/test/reads/S1_R1.fq.gz    | Bin 0 -> 1747 bytes
 .../salmon_tximport/test/reads/S1_R2.fq.gz    | Bin 0 -> 1747 bytes
 .../salmon_tximport/test/reads/S2.fastq.gz    | Bin 1191 -> 0 bytes
 .../salmon_tximport/test/reads/S2_R1.fq.gz    | Bin 0 -> 1739 bytes
 .../salmon_tximport/test/reads/S2_R2.fq.gz    | Bin 0 -> 1749 bytes
 .../salmon_tximport/test/reads/S3.fastq.gz    | Bin 1102 -> 0 bytes
 .../salmon_tximport/test/reads/S4.fastq.gz    | Bin 956 -> 0 bytes
 .../test/resources/genome.fasta.fai           |   1 +
 .../test/resources/transcriptome.fasta        |   5 +-
 .../test/resources/transcriptome.fasta.fai    |   2 +
 test_wrappers.py                              |   2 +-
 16 files changed, 77 insertions(+), 35 deletions(-)
 create mode 100644 meta/bio/salmon_tximport/test/config.yaml
 delete mode 100644 meta/bio/salmon_tximport/test/reads/S1.fastq.gz
 create mode 100644 meta/bio/salmon_tximport/test/reads/S1_R1.fq.gz
 create mode 100644 meta/bio/salmon_tximport/test/reads/S1_R2.fq.gz
 delete mode 100644 meta/bio/salmon_tximport/test/reads/S2.fastq.gz
 create mode 100644 meta/bio/salmon_tximport/test/reads/S2_R1.fq.gz
 create mode 100644 meta/bio/salmon_tximport/test/reads/S2_R2.fq.gz
 delete mode 100644 meta/bio/salmon_tximport/test/reads/S3.fastq.gz
 delete mode 100644 meta/bio/salmon_tximport/test/reads/S4.fastq.gz
 create mode 100644 meta/bio/salmon_tximport/test/resources/genome.fasta.fai
 create mode 100644 meta/bio/salmon_tximport/test/resources/transcriptome.fasta.fai

diff --git a/meta/bio/salmon_tximport/meta.yaml b/meta/bio/salmon_tximport/meta.yaml
index 6ac09a58b77..00b05a75182 100644
--- a/meta/bio/salmon_tximport/meta.yaml
+++ b/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}"``
diff --git a/meta/bio/salmon_tximport/meta_wrapper.smk b/meta/bio/salmon_tximport/meta_wrapper.smk
index 107bfd53e9f..e33f2d4316b 100644
--- a/meta/bio/salmon_tximport/meta_wrapper.smk
+++ b/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:
         "master/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=["S1", "S2"],
         ),
         lib=expand(
-            "pseudo_mapping/{sample}/lib_format_counts.json",
-            sample=["S1", "S2", "S3", "S4"],
+            "<results>/pseudo_mapping/{sample}/lib_format_counts.json",
+            sample=["S1", "S2"],
         ),
         aux_info=expand(
-            "pseudo_mapping/{sample}/aux_info", sample=["S1", "S2", "S3", "S4"]
+            "<results>/pseudo_mapping/{sample}/aux_info",
+            sample=["S1", "S2"],
         ),
         cmd_info=expand(
-            "pseudo_mapping/{sample}/cmd_info.json", sample=["S1", "S2", "S3", "S4"]
+            "<results>/pseudo_mapping/{sample}/cmd_info.json",
+            sample=["S1", "S2"],
         ),
         libparams=expand(
-            "pseudo_mapping/{sample}/libParams", sample=["S1", "S2", "S3", "S4"]
+            "<results>/pseudo_mapping/{sample}/libParams",
+            sample=["S1", "S2"],
         ),
-        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=["S1", "S2"],
+        ),
+        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:
         "master/bio/tximport"
diff --git a/meta/bio/salmon_tximport/test/Snakefile b/meta/bio/salmon_tximport/test/Snakefile
index ef1032f04e9..cd81b946d99 100644
--- a/meta/bio/salmon_tximport/test/Snakefile
+++ b/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: "master/meta/bio/salmon_tximport"
+    meta_wrapper:
+        "master/meta/bio/salmon_tximport"
+    config:
+        config
+
 
-use rule * from salmon_tximport
\ No newline at end of file
+use rule * from salmon_tximport
diff --git a/meta/bio/salmon_tximport/test/config.yaml b/meta/bio/salmon_tximport/test/config.yaml
new file mode 100644
index 00000000000..016d6dd25d3
--- /dev/null
+++ b/meta/bio/salmon_tximport/test/config.yaml
@@ -0,0 +1,9 @@
+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"
diff --git a/meta/bio/salmon_tximport/test/reads/S1.fastq.gz b/meta/bio/salmon_tximport/test/reads/S1.fastq.gz
deleted file mode 100644
index 2c40df8fe838b3d8ddeb7a3be0ff9a5615c896a4..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/meta/bio/salmon_tximport/test/reads/S1_R1.fq.gz b/meta/bio/salmon_tximport/test/reads/S1_R1.fq.gz
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diff --git a/meta/bio/salmon_tximport/test/reads/S1_R2.fq.gz b/meta/bio/salmon_tximport/test/reads/S1_R2.fq.gz
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em~-8V@5oj9*`&<q7~d0mj_42ei~Eny5C8xLDB3^(

diff --git a/meta/bio/salmon_tximport/test/resources/genome.fasta.fai b/meta/bio/salmon_tximport/test/resources/genome.fasta.fai
new file mode 100644
index 00000000000..ade3417e50c
--- /dev/null
+++ b/meta/bio/salmon_tximport/test/resources/genome.fasta.fai
@@ -0,0 +1 @@
+chromosome1	927	13	79	80
diff --git a/meta/bio/salmon_tximport/test/resources/transcriptome.fasta b/meta/bio/salmon_tximport/test/resources/transcriptome.fasta
index 42493ff0db2..7e6c881c561 100644
--- a/meta/bio/salmon_tximport/test/resources/transcriptome.fasta
+++ b/meta/bio/salmon_tximport/test/resources/transcriptome.fasta
@@ -1,4 +1,5 @@
 >transcript1
-CCAGGCTCGTATGTACATCGCTCCTCAAAGTGAGGGGAAGTCCTAAT
+CAGGCTCGTATGTACATCGCTCCTCAAAGTGAGGGGAAGTCCTAATCGG
 >transcript2
-CATCTCCCTGAGTCGGTTTAAAGATTGTCTTGTATGCGTACTCTTGATAGGTAACCCG
+CAGGCTCGTATGTACATCGCTCCTCAAAGTGAGGGGAAGTCCTAATCGGATACCGATTGGACTCTTGAGT
+ACCGGCCCTGT
diff --git a/meta/bio/salmon_tximport/test/resources/transcriptome.fasta.fai b/meta/bio/salmon_tximport/test/resources/transcriptome.fasta.fai
new file mode 100644
index 00000000000..e09f09b0557
--- /dev/null
+++ b/meta/bio/salmon_tximport/test/resources/transcriptome.fasta.fai
@@ -0,0 +1,2 @@
+transcript1	49	13	49	50
+transcript2	81	76	70	71
diff --git a/test_wrappers.py b/test_wrappers.py
index 6b4a32f16f7..3c322c2e734 100644
--- a/test_wrappers.py
+++ b/test_wrappers.py
@@ -1101,7 +1101,7 @@ def test_salmon_tximport_meta(run):
             "--cores",
             "2",
             "--use-conda",
-            "tximport/SummarizedExperimentObject.RDS",
+            "results/tximport/SummarizedExperimentObject.RDS",
         ],
     )
 

From 9da56295d0807768f85c5c846fc170d6f4392109 Mon Sep 17 00:00:00 2001
From: tdayris <thibault.dayris@gustaveroussy.fr>
Date: Fri, 14 Nov 2025 14:22:44 +0100
Subject: [PATCH 2/3] use lookup to answer issue

---
 meta/bio/salmon_tximport/meta_wrapper.smk | 12 ++++++------
 meta/bio/salmon_tximport/test/config.yaml |  5 +++++
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/meta/bio/salmon_tximport/meta_wrapper.smk b/meta/bio/salmon_tximport/meta_wrapper.smk
index 60ffa148d63..f8e1ba88b64 100644
--- a/meta/bio/salmon_tximport/meta_wrapper.smk
+++ b/meta/bio/salmon_tximport/meta_wrapper.smk
@@ -92,27 +92,27 @@ rule tximport:
     input:
         quant=expand(
             "<results>/pseudo_mapping/{sample}/quant.sf",
-            sample=["S1", "S2"],
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         lib=expand(
             "<results>/pseudo_mapping/{sample}/lib_format_counts.json",
-            sample=["S1", "S2"],
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         aux_info=expand(
             "<results>/pseudo_mapping/{sample}/aux_info",
-            sample=["S1", "S2"],
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         cmd_info=expand(
             "<results>/pseudo_mapping/{sample}/cmd_info.json",
-            sample=["S1", "S2"],
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         libparams=expand(
             "<results>/pseudo_mapping/{sample}/libParams",
-            sample=["S1", "S2"],
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         logs=expand(
             "<results>/pseudo_mapping/{sample}/logs",
-            sample=["S1", "S2"],
+            sample=lookup(dpath="salmon_tximport_submodule/samples", within=config),
         ),
         tx_to_gene="<tx_to_gene>",
     output:
diff --git a/meta/bio/salmon_tximport/test/config.yaml b/meta/bio/salmon_tximport/test/config.yaml
index 016d6dd25d3..ddf6a0808a8 100644
--- a/meta/bio/salmon_tximport/test/config.yaml
+++ b/meta/bio/salmon_tximport/test/config.yaml
@@ -7,3 +7,8 @@ pathvars:
   reads_r1: "reads/{sample}_R1.fq.gz"
   reads_r2: "reads/{sample}_R2.fq.gz"
   resources: "resources"
+
+salmon_tximport_submodule:
+  samples:
+    - "S1"
+    - "S2"

From a529cf5eb0860d417ccf9d1239b6aadada59cade Mon Sep 17 00:00:00 2001
From: tdayris <thibault.dayris@gustaveroussy.fr>
Date: Fri, 14 Nov 2025 14:24:19 +0100
Subject: [PATCH 3/3] fmt

---
 meta/bio/salmon_tximport/test/Snakefile | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/meta/bio/salmon_tximport/test/Snakefile b/meta/bio/salmon_tximport/test/Snakefile
index 84fe60bc217..8150a523f73 100644
--- a/meta/bio/salmon_tximport/test/Snakefile
+++ b/meta/bio/salmon_tximport/test/Snakefile
@@ -2,10 +2,15 @@ from snakemake.utils import min_version
 
 min_version("9.13.1")
 
+
 configfile: "config.yaml"
 
+
 module salmon_tximport:
-    meta_wrapper: "file:.."
-    config: config
+    meta_wrapper:
+        "file:.."
+    config:
+        config
+
 
 use rule * from salmon_tximport