feat: add ragtag wrapper

bio/ragtag/correction/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ragtag =2.1.0

bio/ragtag/correction/meta.yaml

@@ -0,0 +1,14 @@
+name: ragtag-correction
+description: Homology-based misassembly correction.
+url: https://github.com/malonge/RagTag/wiki/correct
+authors:
+  - Curro Campuzano Jiménez
+input:
+  - ref: reference fasta file (uncompressed or bgzipped)
+  - query: query fasta file (uncompressed or bgzipped)
+output:
+  - fasta: The corrected query assembly in FASTA format.
+  - agp: The AGP file defining the exact coordinates of query sequence breaks.
+params:
+  - extra: additional parameters
+notes: Multiple threads can be used during Minimap/Unimap alignment. 

bio/ragtag/correction/test/Snakefile

@@ -0,0 +1,14 @@
+rule correction:
+    input:
+        query="fasta/{query}.fasta",
+        ref="fasta/{reference}.fasta",
+    output:
+        fasta="{query}_corrected_{reference}/ragtag.correct.fasta",
+        agp="{query}_corrected_{reference}/ragtag.correct.agp",
+    params:
+        extra="",
+    threads: 16
+    log:
+        "logs/ragtag/{query}_{reference}.log",
+    wrapper:
+        "master/bio/ragtag/correction"

bio/ragtag/correction/test/fasta/query.fasta

@@ -0,0 +1,4 @@
+>sequence A
+ggtaagtcctctagtacaaacacccccaatattgtgatataattaaaattatattcatat
+>sequence B
+ggtaagtgctctagtacaaacacccccaaaaaaaatattgtgatataattaaaattatattcatat

bio/ragtag/correction/test/fasta/reference.fasta

@@ -0,0 +1,7 @@
+>sequence A
+ggtaagtcctctagtacaaacacccccaatattgtgatataattaaaattatattcatat
+tctgttgccagaaaaaacacttttaggctatattagagccatcttctttgaagcgttgtc
+>sequence B
+ggtaagtgctctagtacaaacacccccaatattgtgatataattaaaattatattcatat
+tctgttgccagattttacacttttaggctatattagagccatcttctttgaagcgttgtc
+tatgcatcgatcgacgactg

bio/ragtag/correction/wrapper.py

@@ -0,0 +1,39 @@
+"""Snakemake wrapper for ragtag-correction."""
+
+__author__ = "Curro Campuzano Jiménez"
+__copyright__ = "Copyright 2023, Curro Campuzano Jiménez"
+__email__ = "campuzanocurro@gmail.com"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+import tempfile
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+# Check that two input files were supplied
+n = len(snakemake.input)
+assert n == 2, "Input must contain 2 files. Given: %r." % n
+
+assert snakemake.output.keys(), "Output must contain at least one named file."
+
+valid_keys = ["agp", "fasta"]
+for key in snakemake.output.keys():
+    assert (
+        key in valid_keys
+    ), "Invalid key in output. Valid keys are: %r. Given: %r." % (valid_keys, key)
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "ragtag.py correct"
+        " {snakemake.input.ref}"
+        " {snakemake.input.query}"
+        " {snakemake.params.extra}"
+        " -o {tmpdir} -t {snakemake.threads}"
+        " {log}"
+    )
+
+    for key in valid_keys:
+        outfile = snakemake.output.get(key)
+        if outfile:
+            shell("mv {tmpdir}/ragtag.correct.{key} {outfile}")

bio/ragtag/merge/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ragtag =2.1.0

bio/ragtag/merge/meta.yaml

@@ -0,0 +1,17 @@
+name: ragtag-merge
+description: |
+  Scaffold merging.
+url: https://github.com/malonge/RagTag/wiki/merge
+authors:
+  - Curro Campuzano Jiménez
+input:
+  - ref: assembly fasta file (uncompressed or bgzipped).
+  - agps: scaffolding AGP files.
+  - bam: Optional. Hi-C alignments in BAM format.
+output:
+  - fasta: The merged scaffolds in FASTA format.
+  - agp: The merged scaffold results in AGP format.
+  - links: Optional. If Hi-C alignments in BAM format were given. 
+params:
+  - extra: additional parameters. Do not use with '-b', add the bam file to the input instead.
+notes: |

bio/ragtag/merge/test/Snakefile

@@ -0,0 +1,15 @@
+rule merge:
+    input:
+        fasta="input/{assembly}.fasta",
+        agps=expand("input/{scaffold}.agp", scaffold=["scf1", "scf2"]),
+        #bam = "input/Hi-C.bam",
+    output:
+        fasta="{assembly}_merged.fasta",
+        agp="{assembly}_merged.agp",
+        #links = "{assembly}_merged.links",
+    params:
+        extra="",
+    log:
+        "logs/ragtag/{assembly}_merged.log",
+    wrapper:
+        "master/bio/ragtag/merge"

bio/ragtag/merge/test/input/asm.fasta

@@ -0,0 +1,155 @@
+>NZ_AAJV02000003.1 Escherichia coli E22 gcontig_1112495653270, whole genome shotgun sequence
+TTGGTTGTAACACGGCGTATGGCACATGCGTCGTTAGCGGTCTGGTGACGTTAAAGGGGACAATCCACTC
+CTTGCTCGAGCAAACAAACCAGGTAGCCGGAATGTGCAAGTCAATGATGACGCTGATAAGACGCCTAACC
+AGCGTGGCGATTCGGTTTGACGCCTGGGAAGAGACCAGGGTGCAACGATGAGGGCATTTATGGAACCGCG
+ACAAAGTGTGGTGCCGTAACTGGCTAAGTGCTCTCAGCGTTGTGGTGAATGCGCAGGCTGATGCGCGAAA
+GACATTGCAGCTATTGCGGAAAAGAGCTGTTCGGCGGGGCAATTAAATGCCCGTGAGAGTCTGAAATAAC
+CGCAAGCCGGAGATCAGCACCGGTCACCACAACAGCCACTGCTTTGGCGGTACCAGTTTGTACACTTGCT
+TCCGGCTGGTACCGCTCTTTTTACAAAACAGAGAAGAGCATCACCGGACGACGGGCTCATAACCCAATCC
+ATCCGGGCGGCTGTCACCGCAGGTGTTCTTCTCTGTTTTGTGGAGAAACCAACCGACCTTGCAGGGTCGA
+TATGATGAGGAGCAGCAAAATGGCTAGCGAACGCAGTACTGATGTGCAGGCATTTATCGGGGAGCTGGAC
+GGCGGCGTATTTGAAACCAAAATCGGCGCTGTTCTCAGTGAAGTCGCTTCCGGTGTGATGAACACGAAAA
+CCAAAGGTAAGGTCTCGCTCAACCTGGAAATCGAACCGTTTGATGAGAACCGTGTGAAAATCAAACACAA
+ACTCTCATATGTTCGCCCGACTAACCGCGGGAAAATTTCCGAAGAAGACACCACCGAAACGCCGATGTAT
+GTCAATCGCGGTGGTCGCCTGACTATTCTGCAGGAAGACCAGGGACAATTACTGACTCTTGCCGGTGAAC
+CTGACGGAAAACTCCGCGCAGCAGGTCATTAATATCGTTTTTAATTAACTGATTATTTATCTCATTACTG
+AATATTTTATATAGTGAGGACTTATTATGTCTCAGAACTTAGACGCAACCGCAATTAATCAAATCCATAC
+CCTTATTTCTGCTCAGGGTGTTAATGAAATTATCAGTAAGATTGGTGCCGATGCTGTGGCATTGCCTGAG
+AATTTCCGCATTCATGATCTGGAAAATTTAATTTAAATCGTTTCCGTTTCCGTGGTGCGCTTTCCACTGC
+CAGCATCGATGACTTTACCCGTTATTCTAAAGATCTTGCAGATGAGCACCGCTGCTTTATCGATGCCGAT
+AATATGCGTGCCGTCAGTGTGCTTAACCTAGGTACTATTGATGAACCAGGTCACGCAGATAACACCGCCA
+CTCTCAAACTGAAAAAGACAGCACCGTTCTCTGCTCTGTTGTCTGTTAATGGCGAGCGTAACTCCCAGAA
+GTCACTGGCAGAATGGATTGAAGACTGGGCCGACTACCTTGTGGGCTTTGATGCTAATGGTGACGCCATT
+CAGGCAACAAAAGCAGCTGCGGCAGTCCGTAAAATCACAATTGAAGCAAACCAGACCGCTGATTTTGAAG
+ACAATGACTTCAGCGGCAAACGCTCTCTGATGGAGTCTGTCGAAGCGAAGACCAAAGACATTATGCCAGT
+GGCATTTGAATTTAAATGCGTTCCGTTTGAAGGTCTGAAAGAACGTCCGTTTAAATTACGCCTCAGCATT
+ATCACTGGCGATCGTCCTGTACTGGTTCTGCGCATTATTCAGCTGGAAGCGGTGCAGGAAGAAATGGCTA
+ACGAATTTCGTGATCTGCTTGTTGAGAAATTCAAAGACAGCAAAGTAGAAACCTTTATTGGTACTTTCAC
+CGCCTGATTTCATTACTGCAAATGCCCCTGCGGGGGCATTTATGGAAACGTAATTAACTCAATAATCACC
+GGATGGTGAGGTCTTCCTTTTACCAGAATTCAGCGTGGTGCAGCACATATACGTGGAGAACAAAATGTCA
+TTTATTAAAACTTTTTCCGGGAAGCATTTTTATTATGACAGGATAAATAAAGACGACATCGTGATTAGCG
+ATATCGCGGTTTCCCTTTCAAATATCTGTCGCTTTGCAGGACATCTTTCACACTTCTACAGCGTCGCCCA
+GCATGCGGTGCTTTGCGGCCAGCTGGTGCCGCAGGAATTTGCTTTTGAAGCGTTAATGCATGATGCAACA
+GAAGCGTATTGCCAGGACATCCCAGCTCCACTGAAACGCCTTCTTCCTGACTATAAACGGATGGAAGAAA
+AAATAGACGCCGTAATCCGTGAGAAATACGGGTTACCTCCTGTTATGAGCACGCCAGTGAAATATGCCGA
+TCTCATTATGCTGGCAACCGAACGCCGCGATCTCGGGCTTGATGATGGCTCTTTCTGGCCTGTACTGGAA
+GGTATCCCGGCAACAGAGATGTTCAAAGTTATTCCACTGTCGCCAGGCCATGCCTATGGGATGTTTATGG
+AACGTTTTAACGAGTTATCGGAGTTACGCAAATGCGCATGAATGTTTTCGAAATGGAAGGGTTTCTTCGC
+GGGAAATGTGTACCCCGAGATCTGAAAGTGAATGAAACAAATGCTGAGTACCTGGTACGTAAATTCGATG
+CGCTTGAAGCTAAATGTGCGGCACTGGAAAACAAAATAATACCAGTGTCAGCTGAACTGCCGCCAGCAAA
+TGAAAGTGTTCTGTTATTTGATGCTAACGGAGAAGGCTGGCTAATTGGCTGGCGTTCTCTCTGGTACACC
+TGGGGACAAAAAGAAACCGGAGAATGGCAGTGGACATTTCAGGTCGGGGACCTTGAAAACGTCAATATCA
+CTCACTGGGCAGTAATGCCGAAAGCACCGAAGAATAAAAAATGAGCGTGATAAAAACTCATACAGGAATT
+GTTATCACCCGAGACGGTCCGCAGGTAAAAAAACTGCACCAGACAAAGCGGATGTGGGTCGTCGGAAAAA
+ACGAGTTTTACCACAAAGAAACCGGACGCCGCCACTTTGCAGAAAATACTCGCCGCCGACTGCTGATCGA
+TACCATCAAGCCTATCGAGGTGAAGCATGTTTAAACAGAACGAAAAATCTATCGCTCAAATTGCTGAGTA
+TATCCCGCGTGCGTGCCGGGGTATGCAGTTGCAGGAAGCCAAAGCACGCCTGGAGAAAAAAATTGCGCTC
+TATATCGATGACGGCTGTGATGCCGCCGTTCTTAACGCGGCGTTCGCGCCAGCTCTTAACAGTCATACGC
+GAAAGTCTTTTTTTTCGTGCATCGCAGCGCAGATCCGTAAAGGAGGCAACCAGTGAGCAACATTAACTAT
+CAGGTACTGCGTGAAAAGGCAGAGAAAGCAACTAAAGGAAGCTACATCGTAGGGCATACATCTGTTAACC
+AACACGGCAATTTAACAGGAGTTTTTGTTTGTCAAAAATGGAAAGGAGAACCCGGTGGCGTGATTGCGGA
+ATGTCATGTTAACTGCCTGATTGAATCAGATGCTCAGGCTTATGCAAACGCTGAATTCATAGCAGAGGCT
+AACCCGGCTACCGTGCTGGCACTGCTGGATGAACAGGAAAGAAACCAGCAATACATCAAACGCCGCGACC
+AGGAGAACGAGGATATTGCGCTAACGGTAGGGAAGCTGCGCGTTGAGCTTGAGGAGACAAAATCAAAACT
+CAACGAGCAGCGCGAGTATTACGAGGGAGTTATCTCTGATGGGTGCAAGCGTATTGCTGAACTGGAAGCG
+CGGGAAGTTCAATTACCGACTCGCTACGACCTTCGATATGGACACCCGATAAATGCAGATGAGCGACAAG
+TCATGATACCTAAAGAAAATGGCAGTTGGCTTTACCTGATTGACCTAGAACACGCATTACGCGTCGCTGA
+CATTCGCATCAAAGGAGAGTGATATGGCGTTAACACACCACGAACTCTGTCAGATTGCGTACAAGTTCCT
+TAAGCGCAACGGGTTCAAGGTTTGCTTTCATGACCGCTTTGTTGCTGTAACCAGTACCGGAGAACAGCCA
+GATGCTATGGGATTCAGAAATTCAGCATCATGCCTGATAGAGGCGAAGTGTTCTCGTGCTGACTTGTTGG
+CAGATAGAAAAAAGCGTTTCCGTAAAAATCCCTCACTTGGCATGGGCGACTGGCGATTCTTTATTAGTGA
+GCCGGGAATTATTTCAATTGAGGATTTACCACCTGGCTGGGGATTACTTCACGTTGTTAACGGAAGAGTA
+CGGAAAGTACATGGGTGGCCCAGGGGTAATTGCTGTTGGGGTAATCCTGACGATAAGCCATTTACTGGAA
+ATAAGCAGGTTGAATGCGATTACATGTTATCTGCATTAAGGCGCATGGAGTTGAGAGGGCACCTTAATGA
+AATATATGACGGTGTAATTGTTAATAAGAAAGAAGGAAACGCGGCATGATCACTATTACCAAAGAGCGAC
+TGCTGACAATCAAGCAGTGGCGCGAAACATACGGACCTGATAGCAACGTTGTACTGCCAGCAGAAGAAGC
+GGAAGAACTGGCGCGAATTGCACTGGTATCGCTGGAAGCAGAGCTGGTGGCAAAGATTATAGCTCATTAC
+CCATTAGGAGTTGACGTAGGCAAACAAAAGTTCGTACAGGCCATTGGAGAGCTTCCTGACTTTGGCGGAT
+ATCTATTTGCCGCCCCTCCAGCGCCGATAGTGCCGGAAGAAATGTATTGGCAGGATGCGCCAGTTGAAGG
+CAGCAGCAAAGCGGCTGCATACGCTACAGGCTGGAACGATTGCCGCGAAGCCATGCTTCAGTCCGGAAAC
+TTTCGGGAAAATAAAGATTCGTCAACCAATAATTTTCGGAAAATCCCGGAAGCGTCAACCAGCTCTCCGG
+TAACTCCGGCTCTTCTGCCTGGTGGTTTCACCATTGAGGATGCGAAGGAATTACATGAAGACCTGGCACG
+CAGCCACATAAGCAAGGCCTTAAGTGGCGAAAAGATGAAAAAGAAAGATCGCGATGCTGATTTGCGCTGG
+ATTCATGGCGTTATAGTTCAGGCAGCGTGGTTTGTAAAAGCATCACTGGAGCAGAATGCACTATCGGGCA
+ACTATCCGGTAACTCCGGATAGTTGGATAAGCTGTAGTGAGCGAATGCCGGATAAGTTAATTCCGGTAAT
+GGTCATGTATGAAGACGGTGAGATGTGGTCTGCAATGTGGAATGGCAATCGCTGGGATGATGGCACCGAA
+TATCCGGATCCGCACTCAGTTACGCACTGGCGTGAAATGCCAGCAGCACCGCAGCAGGAGGTGAATCAAT
+GAGCTGGCCTGATGCAATCGTAACTCTGGGGGTGGTATTCGCAGCAGCGTTTGTTGTGTTCTCGATTTGT
+CGATGGGGATAACCACATGTTCGCTTTGATTCAACGCGGGCAGATATACACCGATAGTGCTGGCTACCCG
+ATAAAAATTGTTCGCTGCATAAACAACACAGTGTTGTACAGAAGAATGGATGGGCGAACACAGTCAGTAA
+AAATAAACGATTTCAATGAACGTTTGAACGGATTGATCACCAGGAATACCGACAAATTCTGGCAGAAACA
+GAGCAGGAAGCTCATCTGAAAAAATTACGGGCCATGAAAAGGAAGTAAACAATGAATAAAGCATTTGAAC
+GATGGATACGCCAGCGTTACGGCAATCGCTATGATCTGACGCGAGATGTTGACGGTTTCTACTGTCGTGA
+AGTTGTGAAGCGAATGTTTGAAATGTGGTGCCACTGCCGTGGATGAAAGTTTTATGAGGTTGGCATGCAG
+ACAATCATCTATCAGATAACCCCCAGCAAATGGTGTACGGAGAGAGTCCTTATTGCATCAACAGGGCTAA
+AGCCCGGCACCATCGAGCGGGCCAGAAGAAAGTCATGGATACAGGGAAAAGAATACCGCCATTACTCTGT
+AGAAGGTGATCCGGGGCACTACAGTGAATGCCTGTACAACATCGAAGAGATTATGCGATGGATCGAAAAC
+CAGAAACAACCAGGTGCCAAAAATGCAAGTTCCGGTTAACCTGTTAATGCTCCTGGACGTCTGGGAGGTT
+TAATGAGTAACGCATCATACCCGACAGGCGTTGAAAACCATGGCGGATCACTCCGTATATGGTTTCACTA
+TAATGGCAAACGTGTCAGAGAAAACCTCGGTGTTCCTGACACCGCCAAAAACCGGAAGATCGCAGGTGAA
+CTTCGCACTTCCGTTTGTTTTGCAATCAGAATGGGGAGTTTCGACTACGCCGCGCAGTTCCCTAATTCCC
+CTAACCTGAAACACTTTGGTCTGGGAAAAAGAGAGATAACCGTTAAGGCACTTTCGGAAAAATGGCTTGA
+ACTGAAGAAAATAGAGATTTGTGCGAATGCACTTAATCGTTACCAGTCAGTAATTAAAAACATGTTGCCT
+ATGTTGGGAGAAAAAAAACTAGTTTCATCCATAACAAAAGAGGATTTACTTTTCGCAAGGAGAGATTTGT
+TGACCGGTTACCAAAAGCTTTCTAATGGAAAGACTTCTTCCATAAAAGGGCGCTCAGTGGTCACGGTAAA
+CTACTATATGACAACCATAGCTGGAATGTTTCAATTTGCAACAGATAATGGTTATACCTCAGGAAACCCA
+TTTAACGGTCTGGCACCCTTAAAAAAGTCCAAGGTAAAACCAGATCCTCTCACCCGTGACGAATTTATTC
+GTTTTATTGAGGCTTGCCGTCATCAACAAACAAAAAACCTGTGGATTCTCGCTGTATACACGGGTATTCG
+TCACGGGGAGCTGGTATCGCTGGCATGGGAAGATATAGACCTTAAAGCAAGGACTATAACCATCCGTAGG
+AATTATACAAAACTTGGCGAATTCACTCCACCAAAAACCGATGCAGGCACCGGAAGGACAATTCATCTGG
+TTCAACCAGCTATTGATGCTCTTAAAAGCCAGGCGGAAATGACCATGCTTGGAAAGCAACATTCTGTAGA
+GGTGAAGCAGAGGGAATATGGGAGAACTGCTGTGCATAAATGCACTTTTGTTTTTAGTCCTCAGGTAACA
+AAACAGCAGCAGTTGTCCGGACCTCACTACAAGGTTGACTCCATCAGGGAGTCATGGACAAGTATCTTAA
+AACGCGCAGGTCTGAGACACAGAAAATCGTACCAATCCAGGCATACTTATGCATGCTGGTCACTTGCCGC
+AGGAGCTAATCCTAGTTTTATCGCAAGCCAGATGGGCCACACAAACGCACAAATGGTATTCAATGTTTAC
+GGAGCATGGATGAAAGACAACAATCACGAACAGATAGAACTCCTTAACAAAAGACTATCTGAAAGTGTCC
+CATGTATGCCCCATAAGAAAGCTGGGTAAAATAAAAACTTGCAAAATCAATTAGTTTACCCTTAATCCCT
+GTCACGTTACGCGCGTGGCAGAGGCGTTACGGGTTGCTGAAACCGCAACGGACAGACGGCGGTCATCGAC
+TGTTCAACGATGCCGATATTGACCGTATCCGCGAGATCAAACGCTGGATCGACAACGGCGTGCAGGTCAG
+CAAAGTTAAAATGCTGCTCAGTAATGAAAATGTTGATGTGCAGAACGGCTGGCGCGATCAGCAAGAAACA
+TTACTGACCTACCTGCAAAGCGGCAATCTGCATAGCCTGCGAACGTGGATCAAAGAGCGCGGTCAGGATT
+ACCCCGCCCAGACACTCACCACACATCTGTTTATTCCTCTGCGCCGACGACTTCAATGCCAACAACCGAC
+TCTCCAGGCGCTGCTGGCGATCCTCGACGGCGTACTGATCAACTACATCGCCATTTGTCTGGCTTCGGCA
+CGTAAAAAACAGGGTAAAGATGCGCTGGTGGTTGGCTGGAATATTCAGGATACCACCCGTCTGTGGCTGG
+AGGGCTGGATTGCCAGTCAACAAGGATGGCGCATTGATGTCCTCGCCCACTCGCTCAATCAACTACGCCC
+TGAACTATTCGAAGGCCGTACATTGCTGGTGTGGTGCGGTGAAAATCGAACCTCCGCCCAACAGCAGCAA
+CTCACCAGTTGGCAAGAACAAGGCCATGATATTTTACCACTCGGCATTTAATGATTCGTTAACAAATGCG
+CTTTACTGTACAATCCTTTCGTTAACATAAGGAGTGCATTATGCGCATAGCTAAAATTGGGGTCATCGCC
+CTGTTCCTGTTTATGGCGTTCGGCGGAATTGGTGGCGTCATGCTCGCAGGTTATACCTTTATTTTGCGTG
+CTGGCTAAGCGCCTGCACCAGCCTTTCAAACAGGCGGTCTGCGATGATCGCCGCCAGTGCCACCAGTAAC
+GCCCCCTGGATCACATACGCGGTATTAAATCCGCTAAGCCCGATGATGATGGGCGTACCCAGCGTGCTGG
+CCCCTACCGTTGAGGCGATCGTCGCCGTACCAATGTTGATAATCACCGAAGTTCGCACGCCCGCCAGAAT
+CACCGGAGCCGCCAGCGGTAGCTCGACCTTACGCAGTCGCTGACCACGACTCATTCCCATACCTTTCGCA
+ACTTCTGTCACGCTGGCATCGATCGCTCCCAGCCCGGCAAGTGTCGCCTGCAGGACGGGCAGCACACCGT
+AAAGGATCAAGGCGATAATCGCTGGTTGCAGACCAAAGCCGATCACCGGAACGGCAATCGCCAGCACTGC
+GACAGGCGGAAAAGTCTGTCCAACGGCGGCAATAGTTTCCACCAGTGGGCGAAATTCCGCGCCCCACGGG
+CGAGTGACAGCAATTCCGGCACCAGTGCCAATGATCACCGCAAACAAACTCGAAATTCCCACCAGCCAGA
+AATGAGCCAGTGCCAGAGCTGCAAAACTTTCTTGCTGATAAACGGGTCGTGGCAGTTGTGGGAACAAGGC
+AGCAAACAGCGGCTGGCTGTAAGGCAGCCAGAAAATCAGTGCCACAAACAAAGCAATGAGCCAGAACAGC
+GGATCGCGCAACATCTTCATACGCTTACGCCTCCACCAGCAGATCCTGAAAATGCAGCGTACCGCAAGGC
+TGGCCCTGCGTGTTCACCACCGGCAGCACCTCGCAACCCCGCGCGACAAACAGGGAGAGCGCATCGCGTA
+GCGTCATCTCTTCTACCAGTGCCTCACCTTCTGCCCGTTCTTCGCGACGCACGTAATCCGCCACACTACG
+TAACGAAAGCAGACGCACACCCAGTTCGCTACGTCCAAAAAACTGGCGGACAAAATCATTCGCCGGACGA
+GTCAGCATCGTCAGCGGATTGCCCTGCTGCACCACTTCACCGTGATCCATCAATACCAGATGTTCAGCCA
+GCCGTAGCGCCTCATCAATATCATGAGTGACCAGCACAATAGTGCGCCCCAGCAAACGGTGAATGCGCGT
+CATCTCTTGTTGCAACGCGCCGCGCGTTACCGGGTCCAGTGCGCCAAAAGGTTCATCCATCAGTAAGACT
+TGCGGATCGGCAGCCAGTGCGCGCGCCACTCCCACACGTTGCTGCTGACCACCGGAAAGCTGATGCGGAT
+AACGCTCACGCAAATTTGACTCCAGCCCCAGTAGCGTCATTAATTCGTCGATACGATCGTCAATCCGTGC
+CCGCGACCATTTTTGTAATTGCGGCACGGTAGCGATGTTTTGCGCCACGCTCCAGTGGGGGAACAGGCCA
+ATAGATTGAATGGCATAGCCCATCCGGCGGCGCAACTCCAGTACTGGCAGCGAGCGAATTTCTTCTCCGG
+CAAAGCGGATCTCTCCGCTGTCATGTTCCACCAGGCGGTTAATCATTTTCAAGGTGGTGGATTTGCCGGA
+GCCAGATGTGCCAATCAGCACCGAAAAACTCCCTTCCTGAAAATTGAGATTAAGATCGTTAACGGCTTTT
+TGTGCGCCAAACAGTTTGCTGACATGGCTAAATTCAATCATTACGTTTCACCTTCAGCAGTGCGATAAGC
+AAATCGAACAGGGCATCGATCAGCACCGCCAGAACAATTACCGGGATCACCCCCAGCAACACTAAATCAA
+TGGCGCTGCTTAGCAGCCCCTGGAAAACCAGCGCACCAAAACCGCCTGCGCCGATTAACGCCGCAATCAC
+CGCCATACCTACAGTTTGCACCATCACCACCCGCAGGCTGCGCAGAAATACCGGTAACGCCAGTGGTAAC
+TGAACATGCAGGAATCGCTGCGCCCCGCTCATGCCCATCGCTCTGGCGCTCTCCAGCACATCGCGCGGGA
+TCTGGTTCAAACCGACTACCACGCCGCGCACCAGCGGCAGCAAGGCATAGAGCACCAGCGCAATCAGTGC
+GGGTGTCATTCCGGTTCCTGCTATGCCGAGCTTCCCCAGCCACGGAAAGGCCGTCACCAGCGCGGCAAGC
+GGCGCAATCAACAGGCCAAAGAGCGCCACCGAAGGCACGGTCTGAATGACATTGAGCAGAGAAAAAATTG
+CCCCCTGCCGCGCAGTGGAAAAGTAGCACCAGATGCCCAACGGCACACCAATCACTAACGCAGGCAGCAC
+CGCACCAAACAGCAACGTCAGATGTTGTGCCAGCGCGTCGTCAAACACATCCTGACGGTTGGCGTATTCT
+TTCATTAGTGAGAGATCGTTAAGCGTGCCGGAGTACAGCAACCACAGCGGAATAATGGCAATCTGCATAT
+GCAACAACCAGCGCCACAGCGGATGCGTGGAGATTCGGCGGATGGCATCGCTACAGGCCAGCAATGCCAG
+CGCCGCAGCCAGCCAGAAACCACTGCCGAGGCTGGTACGCGCCAGCGCACTGCCATTTTGCGCCAGTTGG
+GTCGCCGCCTTTCCAGCTCCCCACACCAACAATACGAAGACGAATTGCGCCAGAATGAGTGCACAAATGC

bio/ragtag/merge/test/input/asm.fasta.fai

@@ -0,0 +1 @@
+NZ_AAJV02000003.1	10780	93	70	71

bio/ragtag/merge/test/input/scf1.agp

@@ -0,0 +1,3 @@
+## agp-version 2.1
+# AGP created by RagTag v2.1.0
+seq1_RagTag	1	10780	1	W	NZ_AAJV02000003.1	1	10780	+

bio/ragtag/merge/test/input/scf2.agp

@@ -0,0 +1,3 @@
+## agp-version 2.1
+# AGP created by RagTag v2.1.0
+seq1_RagTag	1	10780	1	W	NZ_AAJV02000003.1	1	10780	+

bio/ragtag/merge/wrapper.py

@@ -0,0 +1,55 @@
+"""Snakemake wrapper for ragtag-merge."""
+
+__author__ = "Curro Campuzano Jiménez"
+__copyright__ = "Copyright 2023, Curro Campuzano Jiménez"
+__email__ = "campuzanocurro@gmail.com"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+import tempfile
+
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+fasta_file = snakemake.input.get("fasta")
+# Check fasta_file is no
+assert fasta_file, "Input must contain only one fasta file."
+
+agp_files = snakemake.input.get("agps")
+
+assert len(agp_files) >= 2, "Input must contain at least 2 agp files. Given: %r." % len(
+    agp_files
+)
+
+bam_file = snakemake.input.get("bam")
+
+# Add Hi-C BAM file to params if present
+if bam_file:
+    snakemake.params.extra += f" -b {bam_file}"
+
+# Raise warning if links file is expected but no Hi-C BAM file is given
+if snakemake.output.get("links") and not bam_file:
+    raise "Links file is present but no Hi-C BAM file is given."
+
+# Check that all keys in snakemake output are valid are either agp, fasta or links
+assert snakemake.output.keys(), "Output must contain at least one named file."
+valid_keys = ["agp", "fasta", "links"]
+for key in snakemake.output.keys():
+    assert (
+        key in valid_keys
+    ), "Invalid key in output. Valid keys are: %r. Given: %r." % (valid_keys, key)
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "ragtag.py merge"
+        " {fasta_file}"
+        " {agp_files}"
+        " {snakemake.params.extra}"
+        " -o {tmpdir}"
+        " {log}"
+    )
+    for key in valid_keys:
+        outfile = snakemake.output.get(key)
+        if outfile:
+            shell("mv {tmpdir}/ragtag.merge.{key} {outfile}")

bio/ragtag/patch/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ragtag =2.1.0

bio/ragtag/patch/meta.yaml

@@ -0,0 +1,20 @@
+name: ragtag-path
+description: Homology-based assembly patching.
+url: https://github.com/malonge/RagTag/wiki/patch
+authors:
+  - Curro Campuzano Jiménez
+input:
+  - ref: reference fasta file (uncompressed or bgzipped)
+  - query: query fasta file (uncompressed or bgzipped)
+output:
+  - fasta: The final FASTA file containing the patched assembly
+  - agp: The final AGP file defining how ragtag.patch.fasta is built.
+  - rename_agp: Optional. An AGP file defining the new names for query sequences
+  - rename_fasta: Optional. A FASTA file with the original query sequence, but with new names.
+  - comps_fasta: Optional. The split target assembly and the renamed query assembly combined into one FASTA file.
+  - ctg_agp: Optional. An AGP file defining how the target assembly was split at gaps
+  - ctg_fasta: Optional. The target assembly split at gaps
+  - asm_dir: Optional. A directory containing Assembly alignment files.
+params:
+  - extra: additional parameters
+notes: Multiple threads can be used during Minimap/Unimap alignment.