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Update published contigs #25

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merged 4 commits into from
Dec 6, 2024
Merged

Update published contigs #25

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6a912f6
Update published contigs
Ge94 Dec 3, 2024
a84b222
Simplified contigs to publish
Ge94 Dec 3, 2024
9bbed3e
Refactor of variables
Ge94 Dec 4, 2024
e831147
replaced published_contigs variable
Ge94 Dec 6, 2024
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14 changes: 7 additions & 7 deletions subworkflows/local/assembly_qc.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ workflow ASSEMBLY_QC {

ch_versions = ch_versions.mix(SEQKIT_SEQ.out.versions)

filtered_contigs = SEQKIT_SEQ.out.fastx
cleaned_contigs = SEQKIT_SEQ.out.fastx

if ( params.remove_human_phix ) {

Expand All @@ -52,10 +52,10 @@ workflow ASSEMBLY_QC {
ch_versions = ch_versions.mix(BLAST_BLASTN_HUMAN_PHIX.out.versions.first())

SEQKIT_GREP_HUMAN_PHIX(
filtered_contigs.join( BLAST_BLASTN_HUMAN_PHIX.out.txt )
cleaned_contigs.join( BLAST_BLASTN_HUMAN_PHIX.out.txt )
)

filtered_contigs = SEQKIT_GREP_HUMAN_PHIX.out.filter
cleaned_contigs = SEQKIT_GREP_HUMAN_PHIX.out.filter

ch_versions = ch_versions.mix(SEQKIT_GREP_HUMAN_PHIX.out.versions)
}
Expand All @@ -68,14 +68,14 @@ workflow ASSEMBLY_QC {
}

BLAST_BLASTN_HOST(
filtered_contigs,
cleaned_contigs,
ch_blast_host_refs
)

ch_versions = ch_versions.mix(BLAST_BLASTN_HOST.out.versions.first())

SEQKIT_GREP_HOST(
filtered_contigs.join( BLAST_BLASTN_HOST.out.txt )
cleaned_contigs.join( BLAST_BLASTN_HOST.out.txt )
)

cleaned_contigs = SEQKIT_GREP_HOST.out.filter
Expand All @@ -84,10 +84,10 @@ workflow ASSEMBLY_QC {
}

PUBLISH_CLEANED_CONTIGS(
filtered_contigs
cleaned_contigs
)

emit:
filtered_contigs = filtered_contigs
cleaned_contigs = cleaned_contigs
versions = ch_versions
}
4 changes: 2 additions & 2 deletions workflows/miassembler.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -246,7 +246,7 @@ workflow MIASSEMBLER {

// Coverage //
ASSEMBLY_COVERAGE(
ASSEMBLY_QC.out.filtered_contigs.join( READS_QC.out.qc_reads, remainder: false ),
ASSEMBLY_QC.out.cleaned_contigs.join( READS_QC.out.qc_reads, remainder: false ),
READS_QC.out.fastp_json
)

Expand All @@ -255,7 +255,7 @@ workflow MIASSEMBLER {
// Stats //
/* The QUAST module was modified to run metaQUAST instead */
QUAST(
ASSEMBLY_QC.out.filtered_contigs,
ASSEMBLY_QC.out.cleaned_contigs,
[ [], [] ], // reference
[ [], [] ] // gff
)
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