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Merged
merged 4 commits into from
Oct 8, 2018
Merged

Assembly graph results #139

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ce4dbdb
Added assembly graph output to publish dir
ODiogoSilva Oct 2, 2018
c6c8826
process to obtain .fastg from megahit (needs refinement)
Oct 6, 2018
ae234ca
added option to generate the fastg files (in megahit_fastg process)
Oct 7, 2018
16bcfb7
cleaned up fastg process code
Oct 8, 2018
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18 changes: 17 additions & 1 deletion flowcraft/generator/components/metagenomics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,6 +139,12 @@ def __init__(self, **kwargs):
"'default', megahit will use the default k-mer lengths. "
"(default: $params.megahitKmers)"
},
"fastg": {
"default": "false",
"description":
"Converts megahit intermediate contigs to fastg"

},
"clearInput": {
"default": "false",
"description":
Expand All @@ -155,7 +161,17 @@ def __init__(self, **kwargs):
"container": "flowcraft/megahit",
"version": "1.1.3-0.1",
"scratch": "true"
}}
},
"megahit_fastg": {
"container": "flowcraft/megahit",
"version": "1.1.3-0.1",
}
}

self.status_channels = [
"megahit",
"megahit_fastg"
]


class Metaspades(Process):
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33 changes: 32 additions & 1 deletion flowcraft/generator/templates/megahit.nf
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Expand Up @@ -23,6 +23,7 @@ process megahit_{{ pid }} {

output:
set sample_id, file('*megahit*.fasta') into {{ output_channel }}
set sample_id, file('megahit/intermediate_contigs/k*.contigs.fa') into IN_fastg{{ pid }}
{% with task_name="megahit" %}
{%- include "compiler_channels.txt" ignore missing -%}
{% endwith %}
Expand All @@ -31,8 +32,38 @@ process megahit_{{ pid }} {
template "megahit.py"

}
IN_fastg = Channel.create()

{{ forks }}
fastg = params.fastg{{ param_id }} ? "true" : "false"
if (fastg) {
process megahit_fastg_{{ pid }}{

// Send POST request to platform
{% include "post.txt" ignore missing %}

tag { sample_id }
publishDir "results/assembly/megahit_{{ pid }}/$sample_id", pattern: "*.fastg"

input:
set sample_id, file(kmer_files) from IN_fastg{{ pid }}

output:
file "*.fastg"
{% with task_name="megahit_fastg" %}
{%- include "compiler_channels.txt" ignore missing -%}
{% endwith %}

script:
"""
for kmer_file in ${kmer_files};
do
echo \$kmer_file
k=\$(echo \$kmer_file | cut -d '.' -f 1);
echo \$k
megahit_toolkit contig2fastg \$k \$kmer_file > \$kmer_file'.fastg';
done
"""
}
}

{{ forks }}
4 changes: 4 additions & 0 deletions flowcraft/generator/templates/spades.nf
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Expand Up @@ -24,6 +24,8 @@ process spades_{{ pid }} {

tag { sample_id }
publishDir 'results/assembly/spades_{{ pid }}/', pattern: '*_spades*.fasta', mode: 'copy'
publishDir "reports/assembly/spades_{{ pid }}/$sample_id", pattern: "*.gfa", mode: "copy"
publishDir "reports/assembly/spades_{{ pid }}/$sample_id", pattern: "*.fastg", mode: "copy"

input:
set sample_id, file(fastq_pair), max_len from {{ input_channel }}.join(SIDE_max_len_{{ pid }})
Expand All @@ -33,6 +35,8 @@ process spades_{{ pid }} {

output:
set sample_id, file('*_spades*.fasta') into {{ output_channel }}
file "*.fastg"
file "*.gfa"
{% with task_name="spades" %}
{%- include "compiler_channels.txt" ignore missing -%}
{% endwith %}
Expand Down