fix: replace ragoo with ragtag (#591)

* replaced ragoo with ragtag and changed env

* changes in benchmarking and report

* fix

* Changed RagTag options

* deactivate non SARS-CoV-2 benchmarking

---------

Co-authored-by: Alexander Thomas <[email protected]>

.github/workflows/main.yml

@@ -203,7 +203,6 @@ jobs:
             benchmark_strain_calling,
             benchmark_assembly,
             benchmark_mixtures,
-            benchmark_non_sars_cov_2,
             benchmark_reads,
             compare_assemblers,
           ]

workflow/envs/ragoo.yaml → workflow/envs/ragtag.yaml

@@ -4,4 +4,4 @@ channels:
   - imperial-college-research-computing
   - nodefaults
 dependencies:
-  - ragoo =1.1
+  - ragtag =2.1

workflow/report/assembly_illumina.rst

@@ -1,3 +1,3 @@
 Assembly of sample {{ snakemake.wildcards.sample }}.
-Reads were assembled with {{ "`metaSPAdes <https://github.com/ablab/spades>`_" if snakemake.params.is_amp else "`Megahit <https://github.com/voutcn/megahit>`_" }}, followed by reference based contig ordering and concatenation with `RaGOO <https://github.com/malonge/RaGOO>`_.
+Reads were assembled with {{ "`metaSPAdes <https://github.com/ablab/spades>`_" if snakemake.params.is_amp else "`Megahit <https://github.com/voutcn/megahit>`_" }}, followed by reference based contig ordering and concatenation with `RagTag <https://github.com/malonge/RagTag>`_.
 Then, assembly was polished by applying variants with an allele frequency of 100% (called by `Varlociraptor <https://varlociraptor.github.io>`_ at FDR 5%).

workflow/report/assembly_ont.rst

@@ -1,2 +1,2 @@
 Assembly of sample {{ snakemake.wildcards.sample }}.
-Reads were assembled with `SPAdes <https://github.com/ablab/spades>`_, followed by reference based contig ordering and concatenation with `RaGOO <https://github.com/malonge/RaGOO>`_.
+Reads were assembled with `SPAdes <https://github.com/ablab/spades>`_, followed by reference based contig ordering and concatenation with `RagTag <https://github.com/malonge/RagTag>`_.

workflow/report/qc-report.rst

@@ -1,3 +1,3 @@
 QC overview for samples from {{ snakemake.wildcards.date }}.
-Readcounts for raw, trimmed and filtered reads, length of initially assembled (`Megahit <https://github.com/voutcn/megahit>`_/`metaSPAdes <https://github.com/ablab/spades>`_) and reference ordered contigs (`RaGOO <https://github.com/malonge/RaGOO>`_).
+Readcounts for raw, trimmed and filtered reads, length of initially assembled (`Megahit <https://github.com/voutcn/megahit>`_/`metaSPAdes <https://github.com/ablab/spades>`_) and reference ordered contigs (`RagTag <https://github.com/malonge/RagTag>`_).
 Percentil overview for contamination in the raw reads (`kraken <https://github.com/DerrickWood/kraken>`_) and called COVID-19-strain including defining SNPs (`Pangolin <https://github.com/cov-lineages/pangolin>`_) and variants of interest from variant calling (`Varlociraptor <https://varlociraptor.github.io>`_).

workflow/rules/assembly.smk

@@ -128,17 +128,17 @@ rule order_contigs:
     output:
         temp("results/{date}/contigs/ordered-unfiltered/{sample}.fasta"),
     log:
-        "logs/{date}/ragoo/{sample}.log",
+        "logs/{date}/ragtag/{sample}.log",
     params:
         outdir=get_output_dir,
     conda:
-        "../envs/ragoo.yaml"
+        "../envs/ragtag.yaml"
     shadow:
         "minimal"
     shell:
         "(mkdir -p {params.outdir}/{wildcards.sample} && cd {params.outdir}/{wildcards.sample} &&"
-        " ragoo.py ../../../../../{input.contigs} ../../../../../{input.reference} &&"
-        " cd ../../../../../ && mv {params.outdir}/{wildcards.sample}/ragoo_output/ragoo.fasta {output})"
+        " ragtag.py scaffold -C -w ../../../../../{input.reference} ../../../../../{input.contigs} &&"
+        " cd ../../../../../ && mv {params.outdir}/{wildcards.sample}/ragtag_output/ragtag.scaffold.fasta {output})"
         " > {log} 2>&1"
 
 
@@ -148,11 +148,11 @@ rule filter_chr0:
     output:
         temp("results/{date}/contigs/ordered/{sample}.fasta"),
     log:
-        "logs/{date}/ragoo/{sample}_cleaned.log",
+        "logs/{date}/ragtag/{sample}_cleaned.log",
     conda:
         "../envs/python.yaml"
     script:
-        "../scripts/ragoo-remove-chr0.py"
+        "../scripts/ragtag-remove-chr0.py"
 
 
 # polish illumina de novo assembly

workflow/rules/benchmarking.smk

@@ -277,17 +277,17 @@ rule order_contigs_assembly_comparison:
             "results/{date}/assembly/{sample}/{assembler}/{sample}.ordered.contigs.fasta"
         ),
     log:
-        "logs/{date}/ragoo/{assembler}/{sample}.log",
+        "logs/{date}/ragtag/{assembler}/{sample}.log",
     params:
         outdir=get_output_dir,
     conda:
-        "../envs/ragoo.yaml"
+        "../envs/ragtag.yaml"
     shadow:
         "minimal"
     shell:
         "(cd {params.outdir} &&"
-        " ragoo.py ../../../../../{input.contigs} ../../../../../{input.reference} &&"
-        " cd ../../../../../ && mv {params.outdir}/ragoo_output/ragoo.fasta {output})"
+        " ragtag.py scaffold -C -w ../../../../../{input.reference} ../../../../../{input.contigs} &&"
+        " cd ../../../../../ && mv {params.outdir}/ragtag_output/ragtag.scaffold.fasta {output})"
         " > {log} 2>&1"
 
 
@@ -297,7 +297,7 @@ use rule filter_chr0 as filter_chr0_assembly_comparison with:
     output:
         "results/{date}/assembly/{sample}/{assembler}/{sample}.contigs.ordered.filtered.fasta",
     log:
-        "logs/{date}/ragoo/{assembler}/{sample}_cleaned.log",
+        "logs/{date}/ragtag/{assembler}/{sample}_cleaned.log",
 
 
 use rule align_contigs as align_contigs_assembly_comparison with:

workflow/scripts/ragoo-remove-chr0.py → workflow/scripts/ragtag-remove-chr0.py

@@ -14,7 +14,7 @@
 
 
 def remove_chr0(data_path, out_path):
-    """This function removes the Chr0 contig generated by raGOO.
+    """This function removes the Chr0 contig generated by ragTag.
     It also renames the id in the FASTA file to the actual sample name.
     In the case where no pseudomolecule is constructed other than the Chr0, it ensures,
     that the FASTA fill contains a 'filler-contig' with a sequence of 'N'.