feat: added Salsa2 wrapper (#532)

* Added Salsa2 wrapper

* Fixed typo

* improve env

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/salsa2/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - salsa2 =2.3

bio/salsa2/meta.yaml

@@ -0,0 +1,15 @@
+name: Salsa2
+description: |
+  A tool to scaffold long read assemblies with Hi-C data
+url: https://github.com/marbl/SALSA
+authors:
+  - Filipe G. Vieira
+input:
+  - BED file
+  - FASTA file
+  - FASTA index file
+output:
+  - polished assembly (FASTA format)
+  - polished assembly (AGP format)
+notes: |
+  * The `extra` param allows for additional program arguments.

bio/salsa2/test/Snakefile

@@ -0,0 +1,17 @@
+rule salsa2:
+    input:
+        fas="{sample}.fasta",
+        fai="{sample}.fasta.fai",
+        bed="{sample}.bed",
+    output:
+        agp="out/{sample}.agp",
+        fas="out/{sample}.fas",
+    log:
+        "logs/salsa2/{sample}.log",
+    params:
+        enzyme="CTTAAG",  # optional
+        extra="--clean yes",  # optional
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/salsa2"

bio/salsa2/test/a.bed

@@ -0,0 +1,2 @@
+lambda_NEB3011_3	89	571	m130725_000747_00121_c100518582550000001823079209281362_s1_p0/15956/701_2749	60	-	89	571	255,0,0	1	482	0
+lambda_NEB3011_3	639	987	m130725_000747_00121_c100518582550000001823079209281362_s1_p0/82740/1942_3951	60	-	639	987	255,0,0	1	348	0

bio/salsa2/test/a.fasta

@@ -0,0 +1,14 @@
+>lambda_NEB3011_3
+AACGGTGTATTACCGGTTTGCTACCAGGGAAGAACGGGAAGGAAAGATGAGCACGAACCTGGTTTTTAAGGAGTGTCGCC
+AGAGTGCCGCGATGAAACGGGTATTGGCGGTATATGGAGTTAAAAGATGACCATCTACATTACTGAGCTAATAACAGGCC
+TGCTGGTAATCGCAGGCCTTTTTATTTGGGGGAGAGGGAAGTCATGAAAAAACTAACCTTTGAAATTCGATCTCCAGCAC
+ATCAGCAAAACGCTATTCACGCAGTACAGCAAATCCTTCCAGACCCAACCAAACCAATCGTAGTAACCATTCAGGAACGC
+AACCGCAGCTTAGACCAAAACAGGAAGCTATGGGCCTGCTTAGGTGACGTCTCTCGTCAGGTTGAATGGCATGGTCGCTG
+GCTGGATGCAGAAAGCTGGAAGTGTGTGTTTACCGCAGCATTAAAGCAGCAGGATGTTGTTCCTAACCTTGCCGGGAATG
+GCTTTGTGGTAATAGGCCAGTCAACCAGCAGGATGCGTGTAGGCGAATTTGCGGAGCTATTAGAGCTTATACAGGCATTC
+GGTACAGAGCGTGGCGTTAAGTGGTCAGACGAAGCGAGACTGGCTCTGGAGTGGAAAGCGAGATGGGGAGACAGGGCTGC
+ATGATAAATGTCGTTAGTTTCTCCGGTGGCAGGACGTCAGCATATTTGCTCTGGCTAATGGAGCAAAAGCGACGGGCAGG
+TAAAGACGTGCATTACGTTTTCATGGATACAGGTTGTGAACATCCAATGACATATCGGTTTGTCAGGGAAGTTGTGAAGT
+TCTGGGATATACCGCTCACCGTATTGCAGGTTGATATCAACCCGGAGCTTGGACAGCCAAATGGTTATACGGTATGGGAA
+CCAAAGGATATTCAGACGCGAATGCCTGTTCTGAAGCCATTTATCGATATGGTAAAGAAATATGGCACTCCATACGTCGG
+CGGCGCGTTCTGCACTGACAGATTAAAACTCGTTCCCTTC

bio/salsa2/test/a.fasta.fai

@@ -0,0 +1 @@
+lambda_NEB3011_3	1000	18	80	81

bio/salsa2/wrapper.py

@@ -0,0 +1,39 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2022, Filipe G. Vieira"
+__license__ = "MIT"
+
+
+import tempfile
+from snakemake.shell import shell
+
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+
+enzyme = snakemake.params.get("enzyme", "")
+if enzyme:
+    enzyme = f"--enzyme {enzyme}"
+
+gfa = snakemake.input.get("gfa", "")
+if gfa:
+    gfa = f"--gfa {gfa}"
+
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "run_pipeline.py"
+        " --assembly {snakemake.input.fas}"
+        " --length {snakemake.input.fai}"
+        " --bed {snakemake.input.bed}"
+        " {enzyme}"
+        " {gfa}"
+        " {extra}"
+        " --output {tmpdir}"
+        " {log}"
+    )
+
+    if snakemake.output.get("agp"):
+        shell("cat {tmpdir}/scaffolds_FINAL.agp > {snakemake.output.agp}")
+    if snakemake.output.get("fas"):
+        shell("cat {tmpdir}/scaffolds_FINAL.fasta > {snakemake.output.fas}")

test.py

@@ -283,6 +283,14 @@ def test_pretext_graph():
     )
 
 
+@skip_if_not_modified
+def test_salsa2():
+    run(
+        "bio/salsa2",
+        ["snakemake", "--cores", "1", "out/a.agp", "--use-conda", "-F"],
+    )
+
+
 @skip_if_not_modified
 def test_mashmap():
     run(