Mercurial > repos > kkonganti > cfsan_cronology

changeset 11:a5f31c44f8c9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
parents ddf7a172bf30
children 78a02e8cb092
files 0.1.0/LICENSE.md 0.1.0/README.md 0.1.0/assets/FDA-CFSAN-Fill.png 0.1.0/assets/FDa-Logo-Blue---medium-01.png 0.1.0/assets/FDa-Logo-replace-Blue-small-01.png 0.1.0/assets/abricate-get_db 0.1.0/assets/abricate_dbs/argannot/sequences 0.1.0/assets/abricate_dbs/argannot/sequences.ndb 0.1.0/assets/abricate_dbs/argannot/sequences.nhd 0.1.0/assets/abricate_dbs/argannot/sequences.nhi 0.1.0/assets/abricate_dbs/argannot/sequences.nhr 0.1.0/assets/abricate_dbs/argannot/sequences.nin 0.1.0/assets/abricate_dbs/argannot/sequences.nog 0.1.0/assets/abricate_dbs/argannot/sequences.not 0.1.0/assets/abricate_dbs/argannot/sequences.nsq 0.1.0/assets/abricate_dbs/argannot/sequences.ntf 0.1.0/assets/abricate_dbs/argannot/sequences.nto 0.1.0/assets/abricate_dbs/megares/sequences 0.1.0/assets/abricate_dbs/megares/sequences.ndb 0.1.0/assets/abricate_dbs/megares/sequences.nhd 0.1.0/assets/abricate_dbs/megares/sequences.nhi 0.1.0/assets/abricate_dbs/megares/sequences.nhr 0.1.0/assets/abricate_dbs/megares/sequences.nin 0.1.0/assets/abricate_dbs/megares/sequences.nog 0.1.0/assets/abricate_dbs/megares/sequences.not 0.1.0/assets/abricate_dbs/megares/sequences.nsq 0.1.0/assets/abricate_dbs/megares/sequences.ntf 0.1.0/assets/abricate_dbs/megares/sequences.nto 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.ndb 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.nhd 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.nhi 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.nhr 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.nin 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.nog 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.not 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.nsq 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.ntf 0.1.0/assets/abricate_dbs/ncbiamrplus/sequences.nto 0.1.0/assets/abricate_dbs/resfinder/sequences 0.1.0/assets/abricate_dbs/resfinder/sequences.ndb 0.1.0/assets/abricate_dbs/resfinder/sequences.nhd 0.1.0/assets/abricate_dbs/resfinder/sequences.nhi 0.1.0/assets/abricate_dbs/resfinder/sequences.nhr 0.1.0/assets/abricate_dbs/resfinder/sequences.nin 0.1.0/assets/abricate_dbs/resfinder/sequences.nog 0.1.0/assets/abricate_dbs/resfinder/sequences.not 0.1.0/assets/abricate_dbs/resfinder/sequences.nsq 0.1.0/assets/abricate_dbs/resfinder/sequences.ntf 0.1.0/assets/abricate_dbs/resfinder/sequences.nto 0.1.0/assets/adaptors.fa 0.1.0/assets/dummy_file.txt 0.1.0/assets/dummy_file2.txt 0.1.0/bin/check_samplesheet.py 0.1.0/bin/create_mqc_data_table.py 0.1.0/bin/dataformat 0.1.0/bin/datasets 0.1.0/bin/dl_pdg_metadata.py 0.1.0/bin/dl_pubmlst_profiles_and_schemes.py 0.1.0/bin/fasta_join.pl 0.1.0/bin/fastq_dir_to_samplesheet.py 0.1.0/bin/filter_genomes_by_qual.py 0.1.0/bin/get_top_unique_mash_hit_genomes.py 0.1.0/bin/index_pdg_metadata.py 0.1.0/bin/qual_confirm.py 0.1.0/bin/rmlst_post.py 0.1.0/bin/stage_ncbi_dataset_genomes.py 0.1.0/conf/base.config 0.1.0/conf/computeinfra.config 0.1.0/conf/fastq.config 0.1.0/conf/logtheseparams.config 0.1.0/conf/manifest.config 0.1.0/conf/modules.config 0.1.0/conf/multiqc/cronology_mqc.yml 0.1.0/cpipes 0.1.0/lib/help/abricate.nf 0.1.0/lib/help/amrfinderplus.nf 0.1.0/lib/help/bbmerge.nf 0.1.0/lib/help/centrifuge.nf 0.1.0/lib/help/checkm2predict.nf 0.1.0/lib/help/dpubmlstpy.nf 0.1.0/lib/help/ectyper.nf 0.1.0/lib/help/fastp.nf 0.1.0/lib/help/flye.nf 0.1.0/lib/help/guncrun.nf 0.1.0/lib/help/kmaalign.nf 0.1.0/lib/help/kmaindex.nf 0.1.0/lib/help/kraken2.nf 0.1.0/lib/help/kronaktimporttext.nf 0.1.0/lib/help/mashscreen.nf 0.1.0/lib/help/mashsketch.nf 0.1.0/lib/help/mashtree.nf 0.1.0/lib/help/masurcapolca.nf 0.1.0/lib/help/megahit.nf 0.1.0/lib/help/mlst.nf 0.1.0/lib/help/pirate.nf 0.1.0/lib/help/polypolish.nf 0.1.0/lib/help/prodigal.nf 0.1.0/lib/help/prokka.nf 0.1.0/lib/help/quast.nf 0.1.0/lib/help/salmonidx.nf 0.1.0/lib/help/seqkitgrep.nf 0.1.0/lib/help/seqkitrmdup.nf 0.1.0/lib/help/seqsero2.nf 0.1.0/lib/help/serotypefinder.nf 0.1.0/lib/help/sfhpy.nf 0.1.0/lib/help/shovill.nf 0.1.0/lib/help/sourmashgather.nf 0.1.0/lib/help/sourmashsearch.nf 0.1.0/lib/help/sourmashsigkmers.nf 0.1.0/lib/help/sourmashsketch.nf 0.1.0/lib/help/sourmashtaxmetagenome.nf 0.1.0/lib/help/spades.nf 0.1.0/lib/help/tuspy.nf 0.1.0/lib/routines.nf 0.1.0/modules/abricate/run/README.md 0.1.0/modules/abricate/run/main.nf 0.1.0/modules/abricate/summary/README.md 0.1.0/modules/abricate/summary/main.nf 0.1.0/modules/cat/fastq/README.md 0.1.0/modules/cat/fastq/main.nf 0.1.0/modules/cat/tables/README.md 0.1.0/modules/cat/tables/main.nf 0.1.0/modules/cat/unique/main.nf 0.1.0/modules/checkm2/predict/main.nf 0.1.0/modules/custom/bwa_idx_mem/main.nf 0.1.0/modules/custom/dump_software_versions/README.md 0.1.0/modules/custom/dump_software_versions/main.nf 0.1.0/modules/custom/dump_software_versions/templates/dumpsoftwareversions.py 0.1.0/modules/custom/qual_passed_genomes/main.nf 0.1.0/modules/download_pdg_metadata/main.nf 0.1.0/modules/download_pubmlst_scheme/main.nf 0.1.0/modules/download_ref_genome/main.nf 0.1.0/modules/fastp/main.nf 0.1.0/modules/filter_pdg_metadata/main.nf 0.1.0/modules/gen_samplesheet/README.md 0.1.0/modules/gen_samplesheet/main.nf 0.1.0/modules/gunc/run/main.nf 0.1.0/modules/index_pdg_metadata/main.nf 0.1.0/modules/kma/align/README.md 0.1.0/modules/kma/align/main.nf 0.1.0/modules/kma/index/README.md 0.1.0/modules/kma/index/main.nf 0.1.0/modules/mash/paste/main.nf 0.1.0/modules/mash/screen/README.md 0.1.0/modules/mash/screen/main.nf 0.1.0/modules/mash/sketch/README.md 0.1.0/modules/mash/sketch/main.nf 0.1.0/modules/mashtree/main.nf 0.1.0/modules/masurca/polish/main.nf 0.1.0/modules/mlst/README.md 0.1.0/modules/mlst/main.nf 0.1.0/modules/multiqc/README.md 0.1.0/modules/multiqc/main.nf 0.1.0/modules/pirate/main.nf 0.1.0/modules/polypolish/main.nf 0.1.0/modules/prodigal/main.nf 0.1.0/modules/prokka/main.nf 0.1.0/modules/quast/main.nf 0.1.0/modules/rmlst/main.nf 0.1.0/modules/samplesheet_check/README.md 0.1.0/modules/samplesheet_check/main.nf 0.1.0/modules/scaffold_genomes/main.nf 0.1.0/modules/seqkit/seq/README.md 0.1.0/modules/seqkit/seq/main.nf 0.1.0/modules/shovill/main.nf 0.1.0/modules/sourmash/gather/main.nf 0.1.0/modules/sourmash/sketch/main.nf 0.1.0/modules/spades/assemble/README.md 0.1.0/modules/spades/assemble/main.nf 0.1.0/modules/top_unique_serovars/main.nf 0.1.0/nextflow.config 0.1.0/readme/centriflaken.md 0.1.0/readme/centriflaken_hy.md 0.1.0/subworkflows/process_fastq.nf 0.1.0/subworkflows/prodka.nf 0.1.0/workflows/conf/cronology.config 0.1.0/workflows/conf/cronology_db.config 0.1.0/workflows/conf/process/cronology.process.config 0.1.0/workflows/conf/process/cronology_db.process.config 0.1.0/workflows/cronology.nf 0.1.0/workflows/cronology_db.nf 0.2.0/CITATION.cff 0.2.0/LICENSE.md 0.2.0/README.md 0.2.0/assets/abricate-get_db 0.2.0/assets/abricate_dbs/argannot/sequences 0.2.0/assets/abricate_dbs/argannot/sequences.ndb 0.2.0/assets/abricate_dbs/argannot/sequences.nhd 0.2.0/assets/abricate_dbs/argannot/sequences.nhi 0.2.0/assets/abricate_dbs/argannot/sequences.nhr 0.2.0/assets/abricate_dbs/argannot/sequences.nin 0.2.0/assets/abricate_dbs/argannot/sequences.nog 0.2.0/assets/abricate_dbs/argannot/sequences.not 0.2.0/assets/abricate_dbs/argannot/sequences.nsq 0.2.0/assets/abricate_dbs/argannot/sequences.ntf 0.2.0/assets/abricate_dbs/argannot/sequences.nto 0.2.0/assets/abricate_dbs/megares/sequences 0.2.0/assets/abricate_dbs/megares/sequences.ndb 0.2.0/assets/abricate_dbs/megares/sequences.nhd 0.2.0/assets/abricate_dbs/megares/sequences.nhi 0.2.0/assets/abricate_dbs/megares/sequences.nhr 0.2.0/assets/abricate_dbs/megares/sequences.nin 0.2.0/assets/abricate_dbs/megares/sequences.nog 0.2.0/assets/abricate_dbs/megares/sequences.not 0.2.0/assets/abricate_dbs/megares/sequences.nsq 0.2.0/assets/abricate_dbs/megares/sequences.ntf 0.2.0/assets/abricate_dbs/megares/sequences.nto 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.ndb 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.nhd 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.nhi 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.nhr 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.nin 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.nog 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.not 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.nsq 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.ntf 0.2.0/assets/abricate_dbs/ncbiamrplus/sequences.nto 0.2.0/assets/abricate_dbs/resfinder/sequences 0.2.0/assets/abricate_dbs/resfinder/sequences.ndb 0.2.0/assets/abricate_dbs/resfinder/sequences.nhd 0.2.0/assets/abricate_dbs/resfinder/sequences.nhi 0.2.0/assets/abricate_dbs/resfinder/sequences.nhr 0.2.0/assets/abricate_dbs/resfinder/sequences.nin 0.2.0/assets/abricate_dbs/resfinder/sequences.nog 0.2.0/assets/abricate_dbs/resfinder/sequences.not 0.2.0/assets/abricate_dbs/resfinder/sequences.nsq 0.2.0/assets/abricate_dbs/resfinder/sequences.ntf 0.2.0/assets/abricate_dbs/resfinder/sequences.nto 0.2.0/assets/adaptors.fa 0.2.0/assets/cronology_on_galaxytrakr.PNG 0.2.0/assets/dummy_file.txt 0.2.0/assets/dummy_file2.txt 0.2.0/assets/microreact_api.key 0.2.0/assets/runs_public_cronobacter.txt 0.2.0/bin/check_samplesheet.py 0.2.0/bin/create_mqc_data_table.py 0.2.0/bin/dataformat 0.2.0/bin/datasets 0.2.0/bin/dl_pdg_metadata.py 0.2.0/bin/dl_pubmlst_profiles_and_schemes.py 0.2.0/bin/fasta_join.pl 0.2.0/bin/fastq_dir_to_samplesheet.py 0.2.0/bin/filter_genomes_by_qual.py 0.2.0/bin/get_top_unique_mash_hit_genomes.py 0.2.0/bin/index_pdg_metadata.py 0.2.0/bin/microreact_post.py 0.2.0/bin/qual_confirm.py 0.2.0/bin/rmlst_post.py 0.2.0/bin/stage_ncbi_dataset_genomes.py 0.2.0/conf/base.config 0.2.0/conf/computeinfra.config 0.2.0/conf/fastq.config 0.2.0/conf/logtheseparams.config 0.2.0/conf/manifest.config 0.2.0/conf/modules.config 0.2.0/conf/multiqc/cronology_mqc.yml 0.2.0/cpipes 0.2.0/lib/help/abricate.nf 0.2.0/lib/help/amrfinderplus.nf 0.2.0/lib/help/bbmerge.nf 0.2.0/lib/help/centrifuge.nf 0.2.0/lib/help/checkm2predict.nf 0.2.0/lib/help/dpubmlstpy.nf 0.2.0/lib/help/ectyper.nf 0.2.0/lib/help/fastp.nf 0.2.0/lib/help/flye.nf 0.2.0/lib/help/guncrun.nf 0.2.0/lib/help/kmaalign.nf 0.2.0/lib/help/kmaindex.nf 0.2.0/lib/help/kraken2.nf 0.2.0/lib/help/kronaktimporttext.nf 0.2.0/lib/help/mashscreen.nf 0.2.0/lib/help/mashsketch.nf 0.2.0/lib/help/mashtree.nf 0.2.0/lib/help/masurcapolca.nf 0.2.0/lib/help/megahit.nf 0.2.0/lib/help/mlst.nf 0.2.0/lib/help/pirate.nf 0.2.0/lib/help/polypolish.nf 0.2.0/lib/help/prodigal.nf 0.2.0/lib/help/prokka.nf 0.2.0/lib/help/quast.nf 0.2.0/lib/help/salmonidx.nf 0.2.0/lib/help/seqkitgrep.nf 0.2.0/lib/help/seqkitrmdup.nf 0.2.0/lib/help/seqsero2.nf 0.2.0/lib/help/serotypefinder.nf 0.2.0/lib/help/sfhpy.nf 0.2.0/lib/help/shovill.nf 0.2.0/lib/help/sourmashgather.nf 0.2.0/lib/help/sourmashsearch.nf 0.2.0/lib/help/sourmashsigkmers.nf 0.2.0/lib/help/sourmashsketch.nf 0.2.0/lib/help/sourmashtaxmetagenome.nf 0.2.0/lib/help/spades.nf 0.2.0/lib/help/tuspy.nf 0.2.0/lib/routines.nf 0.2.0/modules/abricate/run/README.md 0.2.0/modules/abricate/run/main.nf 0.2.0/modules/abricate/summary/README.md 0.2.0/modules/abricate/summary/main.nf 0.2.0/modules/cat/fastq/README.md 0.2.0/modules/cat/fastq/main.nf 0.2.0/modules/cat/tables/README.md 0.2.0/modules/cat/tables/main.nf 0.2.0/modules/cat/unique/main.nf 0.2.0/modules/checkm2/predict/main.nf 0.2.0/modules/custom/bwa_idx_mem/main.nf 0.2.0/modules/custom/dump_software_versions/README.md 0.2.0/modules/custom/dump_software_versions/main.nf 0.2.0/modules/custom/dump_software_versions/templates/dumpsoftwareversions.py 0.2.0/modules/custom/qual_passed_genomes/main.nf 0.2.0/modules/download_pdg_metadata/main.nf 0.2.0/modules/download_pubmlst_scheme/main.nf 0.2.0/modules/download_ref_genome/main.nf 0.2.0/modules/fastp/main.nf 0.2.0/modules/filter_pdg_metadata/main.nf 0.2.0/modules/gen_samplesheet/README.md 0.2.0/modules/gen_samplesheet/main.nf 0.2.0/modules/gunc/run/main.nf 0.2.0/modules/index_pdg_metadata/main.nf 0.2.0/modules/kma/align/README.md 0.2.0/modules/kma/align/main.nf 0.2.0/modules/kma/index/README.md 0.2.0/modules/kma/index/main.nf 0.2.0/modules/mash/paste/main.nf 0.2.0/modules/mash/screen/README.md 0.2.0/modules/mash/screen/main.nf 0.2.0/modules/mash/sketch/README.md 0.2.0/modules/mash/sketch/main.nf 0.2.0/modules/mashtree/main.nf 0.2.0/modules/masurca/polish/main.nf 0.2.0/modules/mlst/README.md 0.2.0/modules/mlst/main.nf 0.2.0/modules/multiqc/README.md 0.2.0/modules/multiqc/main.nf 0.2.0/modules/pirate/main.nf 0.2.0/modules/polypolish/main.nf 0.2.0/modules/prodigal/main.nf 0.2.0/modules/prokka/main.nf 0.2.0/modules/quast/main.nf 0.2.0/modules/rmlst/main.nf