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d4straub

Apply suggestions from code review

Dec 21, 2023

815e62b · Dec 21, 2023

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This branch is 260 commits behind nf-core/ampliseq:master.

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Name		Name	Last commit message	Last commit date
parent directory ..
add_full_sequence_to_taxfile.py		add_full_sequence_to_taxfile.py	Add module to fix fasta input	Feb 23, 2023
add_sh_to_taxonomy.py		add_sh_to_taxonomy.py	Add link to SH file generation	May 25, 2023
combine_table.r		combine_table.r	export relattive abundance two tables with DADA2 or QIIME2 classifica…	Aug 9, 2021
convert_sintax_output.py		convert_sintax_output.py	Change NA to blank in sintax table	May 10, 2023
count_table_minmax_reads.py		count_table_minmax_reads.py	run black	Sep 1, 2022
cutadapt_summary.py		cutadapt_summary.py	run black	Sep 1, 2022
filt_clusters.py		filt_clusters.py	modified to pass lint test	Aug 22, 2023
filt_codon_stats.py		filt_codon_stats.py	Update bin/filt_codon_stats.py	Jun 13, 2023
filt_codons.py		filt_codons.py	fix codon filtering	Aug 31, 2023
filter_stats.py		filter_stats.py	run black	Sep 1, 2022
metadata_all.r		metadata_all.r	fix trailing whitespaces	Jul 27, 2021
metadata_pairwise.r		metadata_pairwise.r	fix trailing whitespaces	Jul 27, 2021
novaseq_err_pe.r		novaseq_err_pe.r	export DADA2 QC svg	Jan 13, 2023
novaseq_err_se.r		novaseq_err_se.r	export DADA2 QC svg	Jan 13, 2023
parse_dada2_taxonomy.r		parse_dada2_taxonomy.r	fix hash and apostrophe in taxonomy strings for QIIME2	Mar 15, 2023
reformat_tax_for_phyloseq.py		reformat_tax_for_phyloseq.py	modified test files for phyloseq and fixed a bug with phyloseq workfl…	Aug 10, 2023
sbdiexport.R		sbdiexport.R	Fix spaces	Jun 29, 2023
sbdiexportreannotate.R		sbdiexportreannotate.R	Add cut_its to SBDI export	Dec 12, 2023
summarize_barrnap.py		summarize_barrnap.py	Sort barrnap columns in summary	Mar 13, 2023
taxref_reformat_coidb.sh		taxref_reformat_coidb.sh	Add config and scripts for coidb	Jan 11, 2023
taxref_reformat_gtdb.sh		taxref_reformat_gtdb.sh	remove any modifications and change taxlevels default to majority	Feb 16, 2023
taxref_reformat_midori2.sh		taxref_reformat_midori2.sh	add species annotation for silva=138 and midori2-co1	Aug 17, 2022
taxref_reformat_phytoref.sh		taxref_reformat_phytoref.sh	Add PhytoRef taxonomy database for chloroplast 16S	Dec 11, 2023
taxref_reformat_pr2.sh		taxref_reformat_pr2.sh	Implement review suggestion	Jun 26, 2023
taxref_reformat_qiime_greengenes2022.sh		taxref_reformat_qiime_greengenes2022.sh	Apply suggestions from code review	Dec 21, 2023
taxref_reformat_qiime_greengenes85.sh		taxref_reformat_qiime_greengenes85.sh	add --qiime_ref_taxonomy	May 28, 2021
taxref_reformat_qiime_silva138.sh		taxref_reformat_qiime_silva138.sh	add --qiime_ref_taxonomy	May 28, 2021
taxref_reformat_qiime_unite.sh		taxref_reformat_qiime_unite.sh	Fix bug in qiime reformatting	May 26, 2023
taxref_reformat_sbdi-gtdb.sh		taxref_reformat_sbdi-gtdb.sh	Update bin/taxref_reformat_sbdi-gtdb.sh	Aug 6, 2021
taxref_reformat_sintax.sh		taxref_reformat_sintax.sh	Add coidb and unite 8.2	Mar 8, 2023
taxref_reformat_standard.sh		taxref_reformat_standard.sh	remove any modifications and change taxlevels default to majority	Feb 16, 2023
taxref_reformat_unite.sh		taxref_reformat_unite.sh	Fix reformatting script for new UNITE	May 25, 2023
taxref_reformat_zehr-nifh.sh		taxref_reformat_zehr-nifh.sh	Fix formatting mistake	Dec 11, 2023
trunclen.py		trunclen.py	fix black formatting	Feb 2, 2023
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