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Enable ext.args to send customized parameters to QUAST modules

enhancementNew feature or requestNew feature or request

Status: Open.

#748 In nf-core/mag;

· amizeranschi opened on Jan 20, 2025

Compress FASTA files with contigs and scaffolds using bgzip instead of gzip, to enable file indexing

enhancementNew feature or requestNew feature or request

Status: Open.

#746 In nf-core/mag;

· amizeranschi opened on Jan 19, 2025

Add new features and Improvement to nf-core/mag: Trimmomatic, contigs param for binning, new concoct default params

enhancementNew feature or requestNew feature or request

Status: Open.

#744 In nf-core/mag;

· Pranjal-Bioinfo opened on Jan 16, 2025

Ensure unique contig names across assemblies, for chaining pipeline with magmap

enhancementNew feature or requestNew feature or request

Status: Open.

#742 In nf-core/mag;

· amizeranschi opened on Jan 6, 2025

Update multiqc config to support new modules

good first issueGood for newcomersGood for newcomers

Status: Open.

#739 In nf-core/mag;

· jfy133 opened on Dec 22, 2024

For unbinned contigs, run CAT in "contig mode" (CAT_pack contigs) instead of "bin mode" (CAT_pack bins)

enhancementNew feature or requestNew feature or request

Status: Open.

#735 In nf-core/mag;

· amizeranschi opened on Dec 17, 2024

Create a summary report

enhancementNew feature or requestNew feature or request

Status: Open.

#728 In nf-core/mag;

· dialvarezs opened on Dec 10, 2024

Consider using Taxometer (From VAMB) for taxonomic classification of metagenomic contigs

enhancementNew feature or requestNew feature or request

Status: Open.

#722 In nf-core/mag;

· jfy133 opened on Dec 3, 2024

Consider binette as alternative bin refinement tool

Status: Open.

#714 In nf-core/mag;

· jfy133 opened on Nov 13, 2024

Be able to run multiple bin QC metrics

enhancementNew feature or requestNew feature or request

Status: Open.

#713 In nf-core/mag;

· harper357 opened on Nov 7, 2024

--host_fasta_bowtie2index path taken for bowtie -S output file

bugSomething isn't workingSomething isn't working

Status: Open.

#694 In nf-core/mag;

· MeriamOs opened on Oct 16, 2024

Optional skipping of short-read input to Filtlong for large datasets

enhancementNew feature or requestNew feature or request

Status: Open.

#691 In nf-core/mag;

· ddomman opened on Oct 14, 2024