From 4e4d04f2bc57dba0e1454516b25780c2128a2a35 Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Mon, 1 Jul 2024 09:46:13 +0930 Subject: [PATCH] Add workflow class and tools --- data/data.yaml | 288 ++++++++++++------------ data/data_workflows.yaml | 450 ++++++++++++++++++++++++++++++++------ finders/common.py | 2 + finders/workflowfinder.py | 8 +- 4 files changed, 532 insertions(+), 216 deletions(-) diff --git a/data/data.yaml b/data/data.yaml index 5dbac09..558bacd 100644 --- a/data/data.yaml +++ b/data/data.yaml @@ -7155,190 +7155,190 @@ - description: 'LAV to BED: Converts a LAV formatted file to BED format' title: LAV to BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=lav_to_bed1 - - description: 'Convert BAM to coordinate-sorted BAM: ' - title: Convert BAM to coordinate-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam - - description: 'Convert CML to SMILES: ' - title: Convert CML to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles + - description: 'Convert BAM to queryname-sorted BAM: ' + title: Convert BAM to queryname-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam + - description: 'Convert Picard Interval List to BED6: converter' + title: Convert Picard Interval List to BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 + - description: 'Convert XTC, DCD, and TRR: ' + title: Convert XTC, DCD, and TRR 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert + - description: 'Convert Genomic Intervals To Strict BED6: ' + title: Convert Genomic Intervals To Strict BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence + taxonomy file to a 2 column mothur taxonomy_outline format' + title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - description: 'OpenBabel converter for molecular formats: ' title: OpenBabel converter for molecular formats 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed - - description: 'Convert plink pbed to ld reduced format: ' - title: Convert plink pbed to ld reduced format 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert - - description: 'Convert Interval to BGZIP: ' - title: Convert Interval to BGZIP 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 - - description: 'Convert compressed and uncompressed BCF files: ' - title: Convert compressed and uncompressed BCF files 0.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + title: Convert compressed file to uncompressed. 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed + - description: 'Convert CRAM to BAM: ' + title: Convert CRAM to BAM 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 + - description: 'Convert Parquet to csv: ' + title: Convert Parquet to csv 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert GFF to BED: ' + title: Convert GFF to BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 + - description: 'Convert CSV to tabular: ' + title: Convert CSV to tabular 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - description: 'Convert uncompressed file to compressed: ' title: Convert uncompressed file to compressed 1.16+galaxy0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - - description: 'Convert tar to directory: ' - title: Convert tar to directory 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory + - description: 'Convert Interval to tabix: ' + title: Convert Interval to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 + - description: 'Convert BAM to BigWig: ' + title: Convert BAM to BigWig 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'Convert compressed file to uncompressed.: ' + title: Convert compressed file to uncompressed. 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed + - description: 'Convert SAM to BAM without sorting: ' + title: Convert SAM to BAM without sorting 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert tabular to dbnsfp: ' + title: Convert tabular to dbnsfp 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp + - description: 'Convert BED to Feature Location Index: ' + title: Convert BED to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - description: 'Convert FASTA to len file: ' title: Convert FASTA to len file 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len - - description: 'Convert Genomic Intervals To BED: ' - title: Convert Genomic Intervals To BED 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 + - description: 'Convert Wiggle to Interval: ' + title: Convert Wiggle to Interval 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 + - description: 'Convert tar to directory: ' + title: Convert tar to directory 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory + - description: 'Convert Interval to BGZIP: ' + title: Convert Interval to BGZIP 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 - description: 'Convert FASTQ files to seek locations: ' title: Convert FASTQ files to seek locations 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 - - description: 'Convert SMILES to MOL: ' - title: Convert SMILES to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - description: 'Convert Genomic Intervals To Strict BED12: ' title: Convert Genomic Intervals To Strict BED12 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 - - description: 'Convert InChI to MOL: ' - title: Convert InChI to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol - - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence - taxonomy file to a 2 column mothur taxonomy_outline format' - title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - - description: 'Convert BAM to queryname-sorted BAM: ' - title: Convert BAM to queryname-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam + - description: 'Convert neostore.zip files to neostore: ' + title: Convert neostore.zip files to neostore 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' title: Convert BigWig to Wiggle 377+galaxy0 url: https://usegalaxy.org.au/root?tool_id=bigwigtowig - - description: 'Convert FASTA to Bowtie base space Index: ' - title: Convert FASTA to Bowtie base space Index 1.3.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - - description: 'Convert Interval to tabix: ' - title: Convert Interval to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 - - description: 'Convert tabular to CSV: ' - title: Convert tabular to CSV 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - - description: 'Convert FASTA to fai file: ' - title: Convert FASTA to fai file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai - - description: 'Convert XTC, DCD, and TRR: ' - title: Convert XTC, DCD, and TRR 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - - description: 'Convert Wiggle to Interval: ' - title: Convert Wiggle to Interval 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - - description: 'Convert compressed file to uncompressed.: ' - title: Convert compressed file to uncompressed. 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed - description: 'Convert GFF to Interval Index: ' title: Convert GFF to Interval Index 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 - - description: 'Convert BGZ VCF to tabix: ' - title: Convert BGZ VCF to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - - description: 'Convert plink pbed to linkage lped: ' - title: Convert plink pbed to linkage lped 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert - - description: 'Convert neostore.zip files to neostore: ' - title: Convert neostore.zip files to neostore 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore + - description: 'Convert tabular to CSV: ' + title: Convert tabular to CSV 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - description: 'Convert BED, GFF, or VCF to BigWig: ' title: Convert BED, GFF, or VCF to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 - - description: 'Convert FASTA to Bowtie color space Index: ' - title: Convert FASTA to Bowtie color space Index 1.2.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert Biom datasets: ' + title: Convert Biom datasets 2.1.5 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom + - description: 'Convert compressed and uncompressed BCF files: ' + title: Convert compressed and uncompressed BCF files 0.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + - description: 'Convert BGZ VCF to tabix: ' + title: Convert BGZ VCF to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 + - description: 'Convert CML to SMILES: ' + title: Convert CML to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - description: 'Convert MAF to Fasta: ' title: Convert MAF to Fasta 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 - - description: 'Convert BAM to BigWig: ' - title: Convert BAM to BigWig 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 - - description: 'Convert SAM to BigWig: ' - title: Convert SAM to BigWig 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - - description: 'Convert Genomic Intervals To Strict BED6: ' - title: Convert Genomic Intervals To Strict BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 - - description: 'Convert GFF to BED: ' - title: Convert GFF to BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_bed_0 - - description: 'Convert CRAM to BAM: ' - title: Convert CRAM to BAM 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 - - description: 'Convert GFF to Feature Location Index: ' - title: Convert GFF to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - - description: 'SMILES to SMILES: ' - title: SMILES to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles - - description: 'Convert FASTA to 2bit: ' - title: Convert FASTA to 2bit 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit - - description: 'Convert BED to Feature Location Index: ' - title: Convert BED to Feature Location Index 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_fli_0 - - description: 'Convert Genomic Intervals To Strict BED: ' - title: Convert Genomic Intervals To Strict BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - - description: 'Convert CSV to tabular: ' - title: Convert CSV to tabular 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - - description: 'Convert Parquet to csv: ' - title: Convert Parquet to csv 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_parquet_to_csv + - description: 'Convert lped to fped: ' + title: Convert lped to fped 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert - description: 'Convert PDB to GRO: ' title: Convert PDB to GRO 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 + - description: 'Convert Genomic Intervals To BED: ' + title: Convert Genomic Intervals To BED 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 + - description: 'Convert FASTA to 2bit: ' + title: Convert FASTA to 2bit 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_2bit + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - description: 'Convert Bam to Bai: ' title: Convert Bam to Bai 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - - description: 'Convert Biom datasets: ' - title: Convert Biom datasets 2.1.5 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom - - description: 'Convert tabular to dbnsfp: ' - title: Convert tabular to dbnsfp 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp - - description: 'Convert BED to GFF: ' - title: Convert BED to GFF 2.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 + - description: 'Convert lped to plink pbed: ' + title: Convert lped to plink pbed 0.02 + url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'Convert SMILES to MOL: ' + title: Convert SMILES to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - description: 'Convert BedGraph to BigWig: ' title: Convert BedGraph to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig - - description: 'Convert Genomic Intervals To Coverage: ' - title: Convert Genomic Intervals To Coverage 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 - - description: 'Convert lped to fped: ' - title: Convert lped to fped 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2fpedconvert - - description: 'Convert SAM to BAM without sorting: ' - title: Convert SAM to BAM without sorting 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert GFF to Feature Location Index: ' + title: Convert GFF to Feature Location Index 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - description: 'Convert MAF to Genomic Intervals: ' title: Convert MAF to Genomic Intervals 1.0.3 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert FASTA to Bowtie base space Index: ' + title: Convert FASTA to Bowtie base space Index 1.3.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - description: 'Convert MOL2 to MOL: ' title: Convert MOL2 to MOL 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - - description: 'Convert Picard Interval List to BED6: converter' - title: Convert Picard Interval List to BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 + - description: 'Convert BED to GFF: ' + title: Convert BED to GFF 2.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_to_gff_0 - description: 'Convert Wiggle to BigWig: ' title: Convert Wiggle to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig + - description: 'Convert Genomic Intervals To Coverage: ' + title: Convert Genomic Intervals To Coverage 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - description: 'Convert GRO to PDB: ' title: Convert GRO to PDB 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 - description: 'Convert Len file to Linecount: ' title: Convert Len file to Linecount 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount - - description: 'Convert FASTA to Tabular: ' - title: Convert FASTA to Tabular 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular - - description: 'Convert lped to plink pbed: ' - title: Convert lped to plink pbed 0.02 - url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert FASTA to fai file: ' + title: Convert FASTA to fai file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 + - description: 'Convert InChI to MOL: ' + title: Convert InChI to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol + - description: 'Convert plink pbed to ld reduced format: ' + title: Convert plink pbed to ld reduced format 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert homepage: '' id: Galaxy CONVERTER license: '' @@ -10541,26 +10541,26 @@ - Evolutionary biology - Sequencing galaxy: - - description: 'ivar consensus: Call consensus from aligned BAM file' - title: ivar consensus 1.4.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_consensus%2Fivar_consensus%2F1.4.2%2Bgalaxy0 + - description: 'ivar variants: Call variants from aligned BAM file' + title: ivar variants 1.4.3+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_variants%2Fivar_variants%2F1.4.3%2Bgalaxy1 - description: 'ivar filtervariants: Filter variants across replicates or multiple samples aligned using the same reference' - title: ivar filtervariants 1.4.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_filtervariants%2Fivar_filtervariants%2F1.4.2%2Bgalaxy0 + title: ivar filtervariants 1.4.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_filtervariants%2Fivar_filtervariants%2F1.4.3%2Bgalaxy0 + - description: 'ivar consensus: Call consensus from aligned BAM file' + title: ivar consensus 1.4.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_consensus%2Fivar_consensus%2F1.4.3%2Bgalaxy0 - description: 'ivar getmasked: Detect primer mismatches and get primer indices for the amplicon to be masked' title: ivar getmasked 1.2.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_getmasked%2Fivar_getmasked%2F1.2.2%2Bgalaxy0 - description: 'ivar removereads: Remove reads from trimmed BAM file' - title: ivar removereads 1.4.2+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_removereads%2Fivar_removereads%2F1.4.2%2Bgalaxy0 + title: ivar removereads 1.4.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_removereads%2Fivar_removereads%2F1.4.3%2Bgalaxy0 - description: 'ivar trim: Trim reads in aligned BAM' title: ivar trim 1.4.2+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_trim%2Fivar_trim%2F1.4.2%2Bgalaxy0 - - description: 'ivar variants: Call variants from aligned BAM file' - title: ivar variants 1.4.2+galaxy1 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fivar_variants%2Fivar_variants%2F1.4.2%2Bgalaxy1 homepage: https://github.com/CGR-UNIMORE/iVar id: ivar license: AGPL-3.0 @@ -22240,8 +22240,8 @@ galaxy: - description: 'TB-Profiler Profile: Infer strain types and drug resistance markers from sequences' - title: TB-Profiler Profile 6.2.1+galaxy0 - url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbprofiler%2Ftb_profiler_profile%2F6.2.1%2Bgalaxy0 + title: TB-Profiler Profile 6.2.1+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ftbprofiler%2Ftb_profiler_profile%2F6.2.1%2Bgalaxy1 homepage: https://github.com/jodyphelan/TBProfiler id: tbprofiler license: GPL-3.0 diff --git a/data/data_workflows.yaml b/data/data_workflows.yaml index ff47247..6c669ee 100644 --- a/data/data_workflows.yaml +++ b/data/data_workflows.yaml @@ -1,4 +1,5 @@ -- doi: 10.48546/workflowhub.workflow.1054.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.1054.1 edam_ops: '' edam_top: '' guide_link: '' @@ -9,9 +10,23 @@ - Galaxy Australia remote_link: '' title: TSI-Scaffolding-with-HiC (based on VGP-HiC-scaffolding) + tools: + - id: https://bio.tools/bwa-mem2 + name: Bwa-mem2 + - id: https://bio.tools/gfastats + name: gfastats + - id: https://bio.tools/busco + name: BUSCO + - id: https://bio.tools/ggplot2 + name: ggplot2 + - id: https://bio.tools/bedtools + name: BEDTools + - id: https://bio.tools/yahs + name: YaHS updated_at: '2024-06-21' url: /workflows/1054?version=1 -- doi: 10.48546/workflowhub.workflow.875.3 +- class: galaxy + doi: 10.48546/workflowhub.workflow.875.3 edam_ops: '' edam_top: '' guide_link: '' @@ -22,9 +37,15 @@ - Galaxy Australia remote_link: '' title: Repeat masking - TSI + tools: + - id: https://bio.tools/repeatmodeler + name: RepeatModeler + - id: https://bio.tools/repeatmasker + name: RepeatMasker updated_at: '2024-06-20' url: /workflows/875?version=3 -- doi: 10.48546/workflowhub.workflow.881.4 +- class: galaxy + doi: 10.48546/workflowhub.workflow.881.4 edam_ops: '' edam_top: '' guide_link: '' @@ -35,9 +56,13 @@ - Galaxy Australia remote_link: '' title: Fgenesh annotation -TSI + tools: + - id: https://bio.tools/busco + name: BUSCO updated_at: '2024-06-18' url: /workflows/881?version=4 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -47,9 +72,11 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: scRNAseq Single Sample Processing Cell Ranger + tools: '' updated_at: '2024-05-30' url: /workflows/647?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Expression analysis edam_top: @@ -62,9 +89,13 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: 'scRNAseq: Count and Load with Cell Ranger' + tools: + - id: https://bio.tools/scanpy + name: SCANPY updated_at: '2024-05-30' url: /workflows/646?version=2 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Expression analysis edam_top: @@ -77,9 +108,11 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: scRNAseq Single Sample Processing Counts Matrix + tools: '' updated_at: '2024-05-30' url: /workflows/514?version=3 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -89,9 +122,11 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: scRNAseq Single Sample Processing STARSolo + tools: '' updated_at: '2024-05-30' url: /workflows/465?version=4 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Expression analysis edam_top: @@ -104,9 +139,13 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: scRNAseq QCtoBasicProcessing + tools: + - id: https://bio.tools/scanpy + name: SCANPY updated_at: '2024-05-30' url: /workflows/468?version=3 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Expression analysis edam_top: @@ -119,9 +158,13 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: scRNAseq CellQC + tools: + - id: https://bio.tools/scanpy + name: SCANPY updated_at: '2024-05-30' url: /workflows/467?version=4 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Expression analysis edam_top: @@ -134,9 +177,15 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: 'scRNAseq: Count and Load with starSOLO' + tools: + - id: https://bio.tools/star + name: STAR + - id: https://bio.tools/scanpy + name: SCANPY updated_at: '2024-05-30' url: /workflows/513?version=3 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Expression analysis edam_top: @@ -149,9 +198,13 @@ - QCIF Bioinformatics remote_link: https://github.com/swbioinf/scrnaseq_howto_ga_workflows.git title: 'scRNAseq: Load counts matrix' + tools: + - id: https://bio.tools/scanpy + name: SCANPY updated_at: '2024-05-30' url: /workflows/512?version=2 -- doi: 10.48546/workflowhub.workflow.880.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.880.1 edam_ops: '' edam_top: '' guide_link: '' @@ -162,9 +215,15 @@ - Galaxy Australia remote_link: '' title: Convert formats - TSI + tools: + - id: https://bio.tools/seqtk + name: seqtk + - id: https://bio.tools/compute_sequence_length + name: compute_sequence_length updated_at: '2024-05-09' url: /workflows/880?version=1 -- doi: 10.48546/workflowhub.workflow.879.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.879.1 edam_ops: '' edam_top: '' guide_link: '' @@ -175,9 +234,15 @@ - Galaxy Australia remote_link: '' title: Extract transcripts - TSI + tools: + - id: https://bio.tools/TransDecoder + name: TransDecoder + - id: https://bio.tools/busco + name: BUSCO updated_at: '2024-05-09' url: /workflows/879?version=1 -- doi: 10.48546/workflowhub.workflow.878.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.878.1 edam_ops: '' edam_top: '' guide_link: '' @@ -188,9 +253,17 @@ - Galaxy Australia remote_link: '' title: Combine transcripts - TSI + tools: + - id: https://bio.tools/stringtie + name: StringTie + - id: https://bio.tools/bedtools + name: BEDTools + - id: https://bio.tools/biopython + name: Biopython updated_at: '2024-05-09' url: /workflows/878?version=1 -- doi: 10.48546/workflowhub.workflow.877.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.877.1 edam_ops: '' edam_top: '' guide_link: '' @@ -201,9 +274,15 @@ - Galaxy Australia remote_link: '' title: Find transcripts - TSI + tools: + - id: https://bio.tools/hisat2 + name: HISAT2 + - id: https://bio.tools/stringtie + name: StringTie updated_at: '2024-05-09' url: /workflows/877?version=1 -- doi: 10.48546/workflowhub.workflow.876.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.876.1 edam_ops: '' edam_top: '' guide_link: '' @@ -214,9 +293,17 @@ - Galaxy Australia remote_link: '' title: QC and trimming of RNAseq reads - TSI + tools: + - id: https://bio.tools/fastqc + name: FastQC + - id: https://bio.tools/trimmomatic + name: Trimmomatic + - id: https://bio.tools/multiqc + name: MultiQC updated_at: '2024-05-09' url: /workflows/876?version=1 -- doi: 10.48546/workflowhub.workflow.836.1 +- class: nextflow + doi: 10.48546/workflowhub.workflow.836.1 edam_ops: '' edam_top: '' guide_link: '' @@ -226,9 +313,11 @@ - Sydney Informatics Hub remote_link: https://github.com/Sydney-Informatics-Hub/Parabricks-Genomics-nf.git title: Parabricks-Genomics-nf + tools: '' updated_at: '2024-04-25' url: /workflows/836?version=1 -- doi: 10.48546/workflowhub.workflow.403.4 +- class: galaxy + doi: 10.48546/workflowhub.workflow.403.4 edam_ops: - Sequence assembly validation edam_top: @@ -240,9 +329,19 @@ - Galaxy Australia remote_link: https://github.com/AustralianBioCommons/Genome-assessment-post-assembly title: Genome-assessment-post-assembly + tools: + - id: https://bio.tools/quast + name: QUAST + - id: https://bio.tools/busco + name: BUSCO + - id: https://bio.tools/merqury + name: Merqury + - id: https://bio.tools/fastx-toolkit + name: FASTX-Toolkit updated_at: '2024-04-19' url: /workflows/403?version=4 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -252,9 +351,19 @@ - Australian BioCommons remote_link: '' title: Genome-assessment-post-assembly + tools: + - id: https://bio.tools/fastx-toolkit + name: FASTX-Toolkit + - id: https://bio.tools/quast + name: QUAST + - id: https://bio.tools/busco + name: BUSCO + - id: https://bio.tools/merqury + name: Merqury updated_at: '2024-03-13' url: /workflows/794?version=1 -- doi: 10.48546/workflowhub.workflow.683.1 +- class: nextflow + doi: 10.48546/workflowhub.workflow.683.1 edam_ops: '' edam_top: '' guide_link: '' @@ -264,9 +373,11 @@ - Australian BioCommons remote_link: https://github.com/eresearchqut/ontvisc.git title: ONTViSc (ONT-based Viral Screening for Biosecurity) + tools: '' updated_at: '2024-02-19' url: /workflows/683?version=1 -- doi: '' +- class: nextflow + doi: '' edam_ops: '' edam_top: - Bioinformatics @@ -279,9 +390,11 @@ - Australian BioCommons remote_link: https://github.com/AusARG/pipesnake title: pipesnake + tools: '' updated_at: '2024-02-08' url: /workflows/737?version=1 -- doi: 10.48546/workflowhub.workflow.691.1 +- class: nextflow + doi: 10.48546/workflowhub.workflow.691.1 edam_ops: '' edam_top: '' guide_link: '' @@ -292,9 +405,11 @@ - Australian BioCommons remote_link: https://github.com/Sydney-Informatics-Hub/Somatic-shortV-nf title: Somatic-ShortV-nf + tools: '' updated_at: '2023-12-20' url: /workflows/691?version=1 -- doi: 10.48546/workflowhub.workflow.431.1 +- class: nextflow + doi: 10.48546/workflowhub.workflow.431.1 edam_ops: '' edam_top: - Bioinformatics @@ -310,9 +425,11 @@ - Australian BioCommons remote_link: https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf title: GermlineStructuralV-nf + tools: '' updated_at: '2023-12-18' url: /workflows/431?version=1 -- doi: 10.48546/workflowhub.workflow.624.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.624.1 edam_ops: - Taxonomic classification edam_top: @@ -325,9 +442,11 @@ - QCIF Bioinformatics remote_link: '' title: Analyses of shotgun metagenomics data with MetaPhlAn2 + tools: '' updated_at: '2024-04-05' url: /workflows/624?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -337,9 +456,11 @@ - QCIF Bioinformatics remote_link: '' title: 'Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]' + tools: '' updated_at: '2023-11-09' url: /workflows/653?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -349,9 +470,11 @@ - QCIF Bioinformatics remote_link: '' title: 'Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]' + tools: '' updated_at: '2023-11-09' url: /workflows/652?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -361,9 +484,11 @@ - QCIF Bioinformatics remote_link: '' title: 'Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]' + tools: '' updated_at: '2023-11-09' url: /workflows/651?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -374,9 +499,11 @@ remote_link: '' title: 'Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]' + tools: '' updated_at: '2023-11-09' url: /workflows/650?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -386,9 +513,11 @@ - QCIF Bioinformatics remote_link: '' title: 'Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]' + tools: '' updated_at: '2023-11-09' url: /workflows/648?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -399,9 +528,11 @@ remote_link: '' title: 'Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur]' + tools: '' updated_at: '2023-11-09' url: /workflows/649?version=1 -- doi: '' +- class: nextflow + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -411,9 +542,11 @@ - Australian BioCommons remote_link: https://github.com/AustralianBioCommons/hifi-assembly-workflow title: HiFi de novo genome assembly workflow + tools: '' updated_at: '2024-02-05' url: /workflows/560?version=1 -- doi: '' +- class: nextflow + doi: '' edam_ops: '' edam_top: - Bioinformatics @@ -429,9 +562,11 @@ - Australian BioCommons remote_link: https://github.com/Sydney-Informatics-Hub/IGVreport-nf title: IGVreport-nf + tools: '' updated_at: '2023-03-21' url: /workflows/440?version=1 -- doi: 10.48546/workflowhub.workflow.221.3 +- class: galaxy + doi: 10.48546/workflowhub.workflow.221.3 edam_ops: - Genome assembly - Sequence assembly validation @@ -446,9 +581,15 @@ - Australian BioCommons remote_link: https://github.com/AustralianBioCommons/PacBio-HiFi-genome-assembly-using-hifiasm title: PacBio HiFi genome assembly using hifiasm v2.1 + tools: + - id: https://bio.tools/hifiadapterfilt + name: HiFiAdapterFilt + - id: https://bio.tools/bandage + name: Bandage updated_at: '2023-01-30' url: /workflows/221?version=3 -- doi: 10.48546/workflowhub.workflow.237.2 +- class: galaxy + doi: 10.48546/workflowhub.workflow.237.2 edam_ops: - Genome assembly - Sequence alignment @@ -463,9 +604,15 @@ - Australian BioCommons remote_link: https://github.com/AustralianBioCommons/Purge-duplicates-from-hifiasm-assembly title: Purge duplicates from hifiasm assembly v1.0 + tools: + - id: https://bio.tools/purge_dups + name: purge_dups + - id: https://bio.tools/minimap2 + name: Minimap2 updated_at: '2023-01-30' url: /workflows/237?version=2 -- doi: 10.48546/workflowhub.workflow.220.2 +- class: galaxy + doi: 10.48546/workflowhub.workflow.220.2 edam_ops: - Conversion - Sequencing quality control @@ -479,9 +626,17 @@ - Galaxy Australia remote_link: https://github.com/AustralianBioCommons/BAM-to-FASTQ-QC title: BAM to FASTQ + QC v1.0 + tools: + - id: https://bio.tools/picard_samtofastq + name: picard_samtofastq + - id: https://bio.tools/samtools + name: SAMtools + - id: https://bio.tools/fastqc + name: FastQC updated_at: '2023-01-30' url: /workflows/220?version=2 -- doi: 10.48546/workflowhub.workflow.393.1 +- class: nextflow + doi: 10.48546/workflowhub.workflow.393.1 edam_ops: '' edam_top: '' guide_link: https://github.com/Sydney-Informatics-Hub/IndexReferenceFasta-nf#user-guide @@ -492,9 +647,11 @@ - Australian BioCommons remote_link: https://github.com/Sydney-Informatics-Hub/IndexReferenceFasta-nf title: IndexReferenceFasta-nf + tools: '' updated_at: '2023-01-16' url: /workflows/393?version=1 -- doi: 10.48546/workflowhub.workflow.146.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.146.1 edam_ops: - Genetic mapping - Mapping @@ -512,9 +669,11 @@ - Sydney Informatics Hub remote_link: '' title: Fastq-to-bam @ NCI-Gadi + tools: '' updated_at: '2023-01-16' url: /workflows/146?version=1 -- doi: 10.48546/workflowhub.workflow.152.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.152.1 edam_ops: - Differential gene expression profiling - Expression analysis @@ -530,9 +689,11 @@ - Sydney Informatics Hub remote_link: '' title: RNASeq-DE @ NCI-Gadi + tools: '' updated_at: '2023-01-16' url: /workflows/152?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Sequence clustering edam_top: @@ -545,9 +706,13 @@ - Australian BioCommons remote_link: https://github.com/AnnaSyme/workflow-partial-gstacks-populations.git title: Partial ref-guided workflow - gstacks and pops + tools: + - id: https://bio.tools/stacks + name: Stacks updated_at: '2023-01-30' url: /workflows/352?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Sequence clustering edam_top: @@ -560,9 +725,17 @@ - Australian BioCommons remote_link: https://github.com/AnnaSyme/workflow-partial-bwa-mem.git title: Partial ref-guided workflow - bwa mem only + tools: + - id: https://bio.tools/bwa-mem2 + name: Bwa-mem2 + - id: https://bio.tools/samtools + name: SAMtools + - id: https://bio.tools/multiqc + name: MultiQC updated_at: '2023-01-30' url: /workflows/351?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Sequence clustering edam_top: @@ -575,9 +748,13 @@ - Australian BioCommons remote_link: https://github.com/AnnaSyme/workflow-partial-cstacks-sstacks-gstacks.git title: 'Partial de novo workflow: c-s-g-pops only' + tools: + - id: https://bio.tools/stacks + name: Stacks updated_at: '2023-01-30' url: /workflows/350?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Sequence clustering edam_top: @@ -590,9 +767,13 @@ - Australian BioCommons remote_link: https://github.com/AnnaSyme/workflow-partial-ustacks-only.git title: 'Partial de novo workflow: ustacks only' + tools: + - id: https://bio.tools/stacks + name: Stacks updated_at: '2023-01-30' url: /workflows/349?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Sequence clustering edam_top: @@ -605,9 +786,13 @@ - Australian BioCommons remote_link: https://github.com/AnnaSyme/workflow-denovo-stacks.git title: Stacks RAD-seq de novo workflow + tools: + - id: https://bio.tools/stacks + name: Stacks updated_at: '2023-01-30' url: /workflows/348?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Sequence clustering edam_top: @@ -620,9 +805,19 @@ - Australian BioCommons remote_link: https://github.com/AnnaSyme/workflow-ref-guided-stacks.git title: Stacks RAD-seq reference-guided workflow + tools: + - id: https://bio.tools/bwa-mem2 + name: Bwa-mem2 + - id: https://bio.tools/samtools + name: SAMtools + - id: https://bio.tools/multiqc + name: MultiQC + - id: https://bio.tools/stacks + name: Stacks updated_at: '2023-01-30' url: /workflows/347?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Sequencing quality control edam_top: @@ -635,9 +830,19 @@ - Australian BioCommons remote_link: https://github.com/AnnaSyme/workflow-qc-of-radseq-reads.git title: QC of RADseq reads + tools: + - id: https://bio.tools/fastqc + name: FastQC + - id: https://bio.tools/cutadapt + name: Cutadapt + - id: https://bio.tools/multiqc + name: MultiQC + - id: https://bio.tools/fastp + name: fastp updated_at: '2023-01-30' url: /workflows/346?version=1 -- doi: 10.48546/workflowhub.workflow.339.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.339.1 edam_ops: - Indel detection - SNP detection @@ -653,9 +858,11 @@ - Sydney Informatics Hub remote_link: https://github.com/Sydney-Informatics-Hub/GermlineShortV_biovalidation.git title: GermlineShortV biovalidation + tools: '' updated_at: '2023-01-16' url: /workflows/339?version=1 -- doi: 10.48546/workflowhub.workflow.327.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.327.1 edam_ops: '' edam_top: - Metagenomic sequencing @@ -668,9 +875,11 @@ - Australian BioCommons remote_link: https://github.com/Sydney-Informatics-Hub/Shotgun-Metagenomics-Analysis.git title: Shotgun-Metagenomics-Analysis + tools: '' updated_at: '2023-01-16' url: /workflows/327?version=1 -- doi: '' +- class: janis + doi: '' edam_ops: '' edam_top: '' guide_link: '' @@ -680,9 +889,11 @@ - Janis remote_link: '' title: Janis Germline Variant-Calling Workflow (GATK) + tools: '' updated_at: '2023-01-16' url: /workflows/236?version=1 -- doi: 10.48546/workflowhub.workflow.230.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.230.1 edam_ops: '' edam_top: '' guide_link: https://doi.org/10.5281/zenodo.5655813 @@ -693,9 +904,11 @@ - Australian BioCommons remote_link: '' title: Combined workflows for large genome assembly + tools: '' updated_at: '2023-01-16' url: /workflows/230?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Taxonomic classification edam_top: @@ -707,9 +920,21 @@ - QCIF Bioinformatics remote_link: '' title: 16S biodiversity for nonoverlap paired end + tools: + - id: https://bio.tools/fastqc + name: FastQC + - id: https://bio.tools/trimmomatic + name: Trimmomatic + - id: https://bio.tools/bwa + name: BWA + - id: https://bio.tools/samtools + name: SAMtools + - id: https://bio.tools/vsearch + name: VSEARCH updated_at: '2024-04-17' url: /workflows/233?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Taxonomic classification edam_top: @@ -721,9 +946,23 @@ - QCIF Bioinformatics remote_link: '' title: 16S biodiversity for overlap paired end + tools: + - id: https://bio.tools/fastqc + name: FastQC + - id: https://bio.tools/trimmomatic + name: Trimmomatic + - id: https://bio.tools/pear + name: PEAR + - id: https://bio.tools/bwa + name: BWA + - id: https://bio.tools/samtools + name: SAMtools + - id: https://bio.tools/vsearch + name: VSEARCH updated_at: '2024-04-17' url: /workflows/232?version=1 -- doi: 10.48546/workflowhub.workflow.229.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.229.1 edam_ops: '' edam_top: - Sequence assembly @@ -735,9 +974,15 @@ - Australian BioCommons remote_link: '' title: Assess genome quality + tools: + - id: https://bio.tools/busco + name: BUSCO + - id: https://bio.tools/quast + name: QUAST updated_at: '2023-01-30' url: /workflows/229?version=1 -- doi: 10.48546/workflowhub.workflow.227.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.227.1 edam_ops: - Sequence assembly validation edam_top: @@ -750,9 +995,15 @@ - Australian BioCommons remote_link: '' title: Racon polish with long reads, x4 + tools: + - id: https://bio.tools/minimap2 + name: Minimap2 + - id: https://bio.tools/Racon + name: Racon updated_at: '2023-01-30' url: /workflows/227?version=1 -- doi: 10.48546/workflowhub.workflow.225.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.225.1 edam_ops: - De-novo assembly edam_top: @@ -765,9 +1016,17 @@ - Australian BioCommons remote_link: '' title: Assembly with Flye + tools: + - id: https://bio.tools/Flye + name: Flye + - id: https://bio.tools/bandage + name: Bandage + - id: https://bio.tools/quast + name: QUAST updated_at: '2023-01-30' url: /workflows/225?version=1 -- doi: 10.48546/workflowhub.workflow.224.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.224.1 edam_ops: - Sequencing quality control edam_top: @@ -780,9 +1039,13 @@ - Australian BioCommons remote_link: '' title: Trim and filter reads - fastp + tools: + - id: https://bio.tools/fastp + name: fastp updated_at: '2023-01-30' url: /workflows/224?version=1 -- doi: 10.48546/workflowhub.workflow.223.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.223.1 edam_ops: - Sequencing quality control edam_top: @@ -795,9 +1058,13 @@ - Australian BioCommons remote_link: '' title: kmer counting - meryl + tools: + - id: https://bio.tools/GenomeScope_2.0 + name: GenomeScope 2.0 updated_at: '2023-01-30' url: /workflows/223?version=1 -- doi: 10.48546/workflowhub.workflow.222.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.222.1 edam_ops: - Sequencing quality control edam_top: @@ -810,9 +1077,17 @@ - Australian BioCommons remote_link: '' title: Data QC + tools: + - id: https://bio.tools/nanoplot + name: NanoPlot + - id: https://bio.tools/fastqc + name: FastQC + - id: https://bio.tools/multiqc + name: MultiQC updated_at: '2023-01-30' url: /workflows/222?version=1 -- doi: 10.48546/workflowhub.workflow.228.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.228.1 edam_ops: - Sequence assembly edam_top: @@ -825,9 +1100,15 @@ - Australian BioCommons remote_link: '' title: Racon polish with Illumina reads, x2 + tools: + - id: https://bio.tools/minimap2 + name: Minimap2 + - id: https://bio.tools/Racon + name: Racon updated_at: '2023-01-30' url: /workflows/228?version=1 -- doi: 10.48546/workflowhub.workflow.226.1 +- class: galaxy + doi: 10.48546/workflowhub.workflow.226.1 edam_ops: - Sequence assembly edam_top: @@ -840,9 +1121,13 @@ - Australian BioCommons remote_link: '' title: Assembly polishing + tools: + - id: https://bio.tools/medaka + name: Medaka updated_at: '2023-01-30' url: /workflows/226?version=1 -- doi: 10.48546/workflowhub.workflow.143.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.143.1 edam_ops: - Indel detection - SNP detection @@ -863,9 +1148,11 @@ - Sydney Informatics Hub remote_link: '' title: Germline-ShortV @ NCI-Gadi + tools: '' updated_at: '2023-01-16' url: /workflows/143?version=1 -- doi: 10.48546/workflowhub.workflow.148.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.148.1 edam_ops: - Genome analysis - Genome comparison @@ -882,9 +1169,11 @@ - Sydney Informatics Hub remote_link: '' title: Somatic-ShortV @ NCI-Gadi + tools: '' updated_at: '2023-01-16' url: /workflows/148?version=1 -- doi: 10.48546/workflowhub.workflow.151.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.151.1 edam_ops: - De-novo assembly - Phasing @@ -899,9 +1188,11 @@ - Sydney Informatics Hub remote_link: '' title: Flashlite-Supernova + tools: '' updated_at: '2023-01-16' url: /workflows/151?version=1 -- doi: 10.48546/workflowhub.workflow.149.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.149.1 edam_ops: - De-novo assembly - Sequence assembly @@ -918,9 +1209,11 @@ - Sydney Informatics Hub remote_link: '' title: Flashlite-Trinity + tools: '' updated_at: '2023-01-16' url: /workflows/149?version=1 -- doi: 10.48546/workflowhub.workflow.150.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.150.1 edam_ops: '' edam_top: - DNA packaging @@ -931,9 +1224,11 @@ - Sydney Informatics Hub remote_link: '' title: Flashlite-Juicer + tools: '' updated_at: '2023-01-16' url: /workflows/150?version=1 -- doi: 10.48546/workflowhub.workflow.153.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.153.1 edam_ops: - Variant calling - Variant filtering @@ -947,9 +1242,11 @@ - Sydney Informatics Hub remote_link: '' title: Bootstrapping-for-BQSR @ NCI-Gadi + tools: '' updated_at: '2023-01-16' url: /workflows/153?version=1 -- doi: 10.48546/workflowhub.workflow.145.1 +- class: shell_script + doi: 10.48546/workflowhub.workflow.145.1 edam_ops: - De-novo assembly - Sequence assembly @@ -964,9 +1261,11 @@ - Sydney Informatics Hub remote_link: '' title: Trinity @ NCI-Gadi + tools: '' updated_at: '2023-01-16' url: /workflows/145?version=1 -- doi: 10.48546/workflowhub.workflow.140.1 +- class: nextflow + doi: 10.48546/workflowhub.workflow.140.1 edam_ops: '' edam_top: '' guide_link: https://github.com/BeatsonLab-MicrobialGenomics/micropipe#micropipe-a-pipeline-for-high-quality-bacterial-genome-construction-using-ont-and-illumina-sequencing @@ -977,9 +1276,11 @@ remote_link: '' title: 'microPIPE: a pipeline for high-quality bacterial genome construction using ONT and Illumina sequencing' + tools: '' updated_at: '2023-01-16' url: /workflows/140?version=1 -- doi: '' +- class: workflow_description_language + doi: '' edam_ops: - Sequence alignment - Variant calling @@ -996,9 +1297,11 @@ - Pawsey Supercomputing Research Centre remote_link: '' title: GATK4 Fastq to joint-called cohort VCF with Cromwell on SLURM + tools: '' updated_at: '2023-01-16' url: /workflows/144?version=1 -- doi: '' +- class: workflow_description_language + doi: '' edam_ops: - Sequence alignment - Variant calling @@ -1016,9 +1319,11 @@ remote_link: '' title: GATK4 Fastq to joint-called cohort VCF with Cromwell on local cluster (no job scheduler) + tools: '' updated_at: '2023-01-16' url: /workflows/147?version=1 -- doi: '' +- class: galaxy + doi: '' edam_ops: - Taxonomic classification edam_top: @@ -1030,9 +1335,11 @@ - Galaxy Australia remote_link: '' title: 16S biodiversity BIOM + tools: '' updated_at: '2024-04-17' url: /workflows/142?version=1 -- doi: '' +- class: nextflow + doi: '' edam_ops: '' edam_top: '' guide_link: https://github.com/marcodelapierre/trinity-nf#trinity-assembly-pipeline-from-usydney-informatics-hub @@ -1042,5 +1349,6 @@ - Australian BioCommons remote_link: '' title: Trinity RNA Assembly + tools: '' updated_at: '2023-01-16' url: /workflows/114?version=2 diff --git a/finders/common.py b/finders/common.py index 4d60cb9..6f580e7 100644 --- a/finders/common.py +++ b/finders/common.py @@ -44,6 +44,8 @@ class FIELD_NAMES(Enum): URL = "FIELD_NAMES.URL" LAUNCH_LINK = "FIELD_NAMES.LAUNCH_LINK" GUIDE_LINK = "FIELD_NAMES.GUIDE_LINK" + WORKFLOW_CLASS = "FIELD_NAMES.WORKFLOW_CLASS" + WORKFLOW_TOOLS = "FIELD_NAMES.WORKFLOW_TOOLS" def __init__(self): self.identifier = "" diff --git a/finders/workflowfinder.py b/finders/workflowfinder.py index 4dd2cd4..850f811 100644 --- a/finders/workflowfinder.py +++ b/finders/workflowfinder.py @@ -87,6 +87,8 @@ def _render(self, data): workflow_attr = data["data"]["attributes"] if workflow_attr["title"]: retval[Dataprovider.FIELD_NAMES.TITLE] = (workflow_attr["title"]).replace("_", " ") + if workflow_attr['workflow_class']: + retval[Dataprovider.FIELD_NAMES.WORKFLOW_CLASS] = workflow_attr['workflow_class']['key'] if workflow_attr["license"]: retval[Dataprovider.FIELD_NAMES.LICENSE] = workflow_attr["license"] #if workflow_attr["description"]: @@ -101,6 +103,8 @@ def _render(self, data): retval[Dataprovider.FIELD_NAMES.EDAM_OPS] = workflow_attr["operation_annotations"] if workflow_attr["topic_annotations"]: retval[Dataprovider.FIELD_NAMES.EDAM_TOP] = workflow_attr["topic_annotations"] + if workflow_attr["tools"]: + retval[Dataprovider.FIELD_NAMES.WORKFLOW_TOOLS] = workflow_attr["tools"] workflow_links = data["data"]["links"] if workflow_links["self"]: retval[Dataprovider.FIELD_NAMES.URL] = workflow_links["self"] @@ -173,6 +177,7 @@ def translate_doi(val): # see https://stackoverflow.com/a/9285148 # see https://stackoverflow.com/a/62014515 "title": workflow.get(Dataprovider.FIELD_NAMES.TITLE, ""), + "class": workflow.get(Dataprovider.FIELD_NAMES.WORKFLOW_CLASS, ""), "url": workflow.get(Dataprovider.FIELD_NAMES.URL, ""), "remote_link": workflow.get(Dataprovider.FIELD_NAMES.REMOTE_LINK, ""), "edam_top": [i["label"] for i in workflow[ @@ -186,7 +191,8 @@ def translate_doi(val): "doi": workflow.get(Dataprovider.FIELD_NAMES.DOI, ""), "projects": [i for i in workflow[Dataprovider.FIELD_NAMES.PROJECTS]] if isinstance(workflow[Dataprovider.FIELD_NAMES.PROJECTS], list) else "", "guide_link": workflow.get(Dataprovider.FIELD_NAMES.GUIDE_LINK, ""), - "launch_link": workflow.get(Dataprovider.FIELD_NAMES.LAUNCH_LINK, "") + "launch_link": workflow.get(Dataprovider.FIELD_NAMES.LAUNCH_LINK, ""), + "tools": workflow.get(Dataprovider.FIELD_NAMES.WORKFLOW_TOOLS, "") }