From 93fc7a6531e7a526d8744189994283aea738e6bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 20 Apr 2022 13:21:47 +0200 Subject: [PATCH 1/2] add missing assets --- asset_pep/assets.csv | 22 +++++++++++++++++++++- asset_pep/recipe_inputs.csv | 32 ++++++++++++++++++++++++++++++++ 2 files changed, 53 insertions(+), 1 deletion(-) diff --git a/asset_pep/assets.csv b/asset_pep/assets.csv index 4529b26..81508ee 100644 --- a/asset_pep/assets.csv +++ b/asset_pep/assets.csv @@ -46,4 +46,24 @@ caenorhabditis_elegans-ensembl-wbcel235,bwa_index caenorhabditis_elegans-ensembl-wbcel215,fasta caenorhabditis_elegans-ensembl-wbcel215,bowtie2_index caenorhabditis_elegans-ensembl-wbcel215,gtf -caenorhabditis_elegans-ensembl-wbcel215,bwa_index \ No newline at end of file +caenorhabditis_elegans-ensembl-wbcel215,bwa_index +homo_sapiens-ncbi-grch38,star_index +homo_sapiens-ncbi-grch38,bismark_bt2_index +homo_sapiens-ncbi-grch38,gencode_gtf +homo_sapiens-ncbi-grch38,bed12 +homo_sapiens-ucsc-hg38,star_index +homo_sapiens-ucsc-hg38,bismark_bt2_index +homo_sapiens-ucsc-hg38,gencode_gtf +homo_sapiens-ucsc-hg38,bed12 +homo_sapiens-ucsc-hg19,star_index +homo_sapiens-ucsc-hg19,bismark_bt2_index +homo_sapiens-ucsc-hg19,gencode_gtf +homo_sapiens-ucsc-hg19,bed12 +caenorhabditis_elegans-ensembl-wbcel235,star_index +caenorhabditis_elegans-ensembl-wbcel235,bismark_bt2_index +caenorhabditis_elegans-ensembl-wbcel235,gencode_gtf +caenorhabditis_elegans-ensembl-wbcel235,bed12 +caenorhabditis_elegans-ucsc-ce10,star_index +caenorhabditis_elegans-ucsc-ce10,bismark_bt2_index +caenorhabditis_elegans-ucsc-ce10,gencode_gtf +caenorhabditis_elegans-ucsc-ce10,bed12 diff --git a/asset_pep/recipe_inputs.csv b/asset_pep/recipe_inputs.csv index d07f2cf..52bccb5 100644 --- a/asset_pep/recipe_inputs.csv +++ b/asset_pep/recipe_inputs.csv @@ -7,3 +7,35 @@ homo_sapiens-ucsc-hg38-fasta,fasta,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/ homo_sapiens-ucsc-hg38-gtf,gtf,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf,files, homo_sapiens-ucsc-hg19-fasta,fasta,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa,files, homo_sapiens-ucsc-hg19-gtf,gtf,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf,files, +homo_sapiens-ncbi-grch38-bwa_index,bwa_index,fasta,assets, +homo_sapiens-ncbi-grch38-bowtie2_index,bowtie2_index,fasta,assets, +homo_sapiens-ncbi-grch38-star_index,star_index,fasta,assets, +homo_sapiens-ncbi-grch38-bismark_bt2_index,bismark_bt2_index,fasta,assets, +homo_sapiens-ncbi-grch38-gencode_gtf,gencode_gtf,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf,files, +homo_sapiens-ncbi-grch38-bed12,bed12,s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed,files, +homo_sapiens-ucsc-hg38-bwa_index,bwa_index,fasta,assets, +homo_sapiens-ucsc-hg38-bowtie2_index,bowtie2_index,fasta,assets, +homo_sapiens-ucsc-hg38-star_index,star_index,fasta,assets, +homo_sapiens-ucsc-hg38-bismark_bt2_index,bismark_bt2_index,fasta,assets, +homo_sapiens-ucsc-hg38-gencode_gtf,gencode_gtf,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf,files, +homo_sapiens-ucsc-hg38-bed12,bed12,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed,files, +homo_sapiens-ucsc-hg19-bwa_index,bwa_index,fasta,assets, +homo_sapiens-ucsc-hg19-bowtie2_index,bowtie2_index,fasta,assets, +homo_sapiens-ucsc-hg19-star_index,star_index,fasta,assets, +homo_sapiens-ucsc-hg19-bismark_bt2_index,bismark_bt2_index,fasta,assets, +homo_sapiens-ucsc-hg19-gencode_gtf,gencode_gtf,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf,files, +homo_sapiens-ucsc-hg19-bed12,bed12,s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed,files, +caenorhabditis_elegans-ensembl-wbcel235-fasta,fasta,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa,files, +caenorhabditis_elegans-ensembl-wbcel235-bwa_index,bwa_index,fasta,assets, +caenorhabditis_elegans-ensembl-wbcel235-bowtie2_index,bowtie2_index,fasta,assets, +caenorhabditis_elegans-ensembl-wbcel235-star_index,star_index,fasta,assets, +caenorhabditis_elegans-ensembl-wbcel235-bismark_bt2_index,bismark_bt2_index,fasta,assets, +caenorhabditis_elegans-ensembl-wbcel235-gencode_gtf,gencode_gtf,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf,files, +caenorhabditis_elegans-ensembl-wbcel235-bed12,bed12,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed,files, +caenorhabditis_elegans-ucsc-ce10-fasta,fasta,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa,files, +caenorhabditis_elegans-ucsc-ce10-bwa_index,bwa_index,fasta,assets, +caenorhabditis_elegans-ucsc-ce10-bowtie2_index,bowtie2_index,fasta,assets, +caenorhabditis_elegans-ucsc-ce10-star_index,star_index,fasta,assets, +caenorhabditis_elegans-ucsc-ce10-bismark_bt2_index,bismark_bt2_index,fasta,assets, +caenorhabditis_elegans-ucsc-ce10-gencode_gtf,gencode_gtf,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf,files, +caenorhabditis_elegans-ucsc-ce10-bed12,bed12,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed,files, From da8d9926ce8590bc4c49a0556bea48550900f16b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 3 May 2022 13:13:20 +0200 Subject: [PATCH 2/2] add assets for missing genomes --- asset_pep/assets.csv | 229 ++++++++++++++++++++++++++++++++++++ asset_pep/recipe_inputs.csv | 229 ++++++++++++++++++++++++++++++++++++ 2 files changed, 458 insertions(+) diff --git a/asset_pep/assets.csv b/asset_pep/assets.csv index 81508ee..2a68405 100644 --- a/asset_pep/assets.csv +++ b/asset_pep/assets.csv @@ -67,3 +67,232 @@ caenorhabditis_elegans-ucsc-ce10,star_index caenorhabditis_elegans-ucsc-ce10,bismark_bt2_index caenorhabditis_elegans-ucsc-ce10,gencode_gtf caenorhabditis_elegans-ucsc-ce10,bed12 +homo_sapiens-ensembl-grch37,fasta +homo_sapiens-ensembl-grch37,bwa_index +homo_sapiens-ensembl-grch37,bowtie2_index +homo_sapiens-ensembl-grch37,star_index +homo_sapiens-ensembl-grch37,bismark_bt2_index +homo_sapiens-ensembl-grch37,gencode_gtf +homo_sapiens-ensembl-grch37,bed12 +mus_musculus-ensembl-grcm38,fasta +mus_musculus-ensembl-grcm38,bwa_index +mus_musculus-ensembl-grcm38,bowtie2_index +mus_musculus-ensembl-grcm38,star_index +mus_musculus-ensembl-grcm38,bismark_bt2_index +mus_musculus-ensembl-grcm38,gencode_gtf +mus_musculus-ensembl-grcm38,bed12 +mus_musculus-ucsc-mm10,fasta +mus_musculus-ucsc-mm10,bwa_index +mus_musculus-ucsc-mm10,bowtie2_index +mus_musculus-ucsc-mm10,star_index +mus_musculus-ucsc-mm10,bismark_bt2_index +mus_musculus-ucsc-mm10,gencode_gtf +mus_musculus-ucsc-mm10,bed12 +arabidopsis_thaliana-ensembl-tair10,fasta +arabidopsis_thaliana-ensembl-tair10,bwa_index +arabidopsis_thaliana-ensembl-tair10,bowtie2_index +arabidopsis_thaliana-ensembl-tair10,star_index +arabidopsis_thaliana-ensembl-tair10,bismark_bt2_index +arabidopsis_thaliana-ensembl-tair10,gencode_gtf +arabidopsis_thaliana-ensembl-tair10,bed12 +bacillus_subtilis_168-ensembl-eb2,fasta +bacillus_subtilis_168-ensembl-eb2,bwa_index +bacillus_subtilis_168-ensembl-eb2,bowtie2_index +bacillus_subtilis_168-ensembl-eb2,star_index +bacillus_subtilis_168-ensembl-eb2,bismark_bt2_index +bacillus_subtilis_168-ensembl-eb2,gencode_gtf +bacillus_subtilis_168-ensembl-eb2,bed12 +bos_taurus-ensembl-umd31,fasta +bos_taurus-ensembl-umd31,bwa_index +bos_taurus-ensembl-umd31,bowtie2_index +bos_taurus-ensembl-umd31,star_index +bos_taurus-ensembl-umd31,bismark_bt2_index +bos_taurus-ensembl-umd31,gencode_gtf +bos_taurus-ensembl-umd31,bed12 +bos_taurus-ucsc-bostau8,fasta +bos_taurus-ucsc-bostau8,bwa_index +bos_taurus-ucsc-bostau8,bowtie2_index +bos_taurus-ucsc-bostau8,star_index +bos_taurus-ucsc-bostau8,bismark_bt2_index +bos_taurus-ucsc-bostau8,gencode_gtf +bos_taurus-ucsc-bostau8,bed12 +canis_familiaris-ensembl-canfam31,fasta +canis_familiaris-ensembl-canfam31,bwa_index +canis_familiaris-ensembl-canfam31,bowtie2_index +canis_familiaris-ensembl-canfam31,star_index +canis_familiaris-ensembl-canfam31,bismark_bt2_index +canis_familiaris-ensembl-canfam31,gencode_gtf +canis_familiaris-ensembl-canfam31,bed12 +canis_familiaris-ucsc-canfam3,fasta +canis_familiaris-ucsc-canfam3,bwa_index +canis_familiaris-ucsc-canfam3,bowtie2_index +canis_familiaris-ucsc-canfam3,star_index +canis_familiaris-ucsc-canfam3,bismark_bt2_index +canis_familiaris-ucsc-canfam3,gencode_gtf +canis_familiaris-ucsc-canfam3,bed12 +danio_rerio-ensembl-grcz10,fasta +danio_rerio-ensembl-grcz10,bwa_index +danio_rerio-ensembl-grcz10,bowtie2_index +danio_rerio-ensembl-grcz10,star_index +danio_rerio-ensembl-grcz10,bismark_bt2_index +danio_rerio-ensembl-grcz10,gencode_gtf +danio_rerio-ensembl-grcz10,bed12 +danio_rerio-ucsc-danrer10,fasta +danio_rerio-ucsc-danrer10,bwa_index +danio_rerio-ucsc-danrer10,bowtie2_index +danio_rerio-ucsc-danrer10,star_index +danio_rerio-ucsc-danrer10,bismark_bt2_index +danio_rerio-ucsc-danrer10,gencode_gtf +danio_rerio-ucsc-danrer10,bed12 +drosophila_melanogaster-ensembl-bdgp6,fasta +drosophila_melanogaster-ensembl-bdgp6,bwa_index +drosophila_melanogaster-ensembl-bdgp6,bowtie2_index +drosophila_melanogaster-ensembl-bdgp6,star_index +drosophila_melanogaster-ensembl-bdgp6,bismark_bt2_index +drosophila_melanogaster-ensembl-bdgp6,gencode_gtf +drosophila_melanogaster-ensembl-bdgp6,bed12 +drosophila_melanogaster-ucsc-dm6,fasta +drosophila_melanogaster-ucsc-dm6,bwa_index +drosophila_melanogaster-ucsc-dm6,bowtie2_index +drosophila_melanogaster-ucsc-dm6,star_index +drosophila_melanogaster-ucsc-dm6,bismark_bt2_index +drosophila_melanogaster-ucsc-dm6,gencode_gtf +drosophila_melanogaster-ucsc-dm6,bed12 +equus_caballus-ensembl-equcab2,fasta +equus_caballus-ensembl-equcab2,bwa_index +equus_caballus-ensembl-equcab2,bowtie2_index +equus_caballus-ensembl-equcab2,star_index +equus_caballus-ensembl-equcab2,bismark_bt2_index +equus_caballus-ensembl-equcab2,gencode_gtf +equus_caballus-ensembl-equcab2,bed12 +equus_caballus-ucsc-equcab2,fasta +equus_caballus-ucsc-equcab2,bwa_index +equus_caballus-ucsc-equcab2,bowtie2_index +equus_caballus-ucsc-equcab2,star_index +equus_caballus-ucsc-equcab2,bismark_bt2_index +equus_caballus-ucsc-equcab2,gencode_gtf +equus_caballus-ucsc-equcab2,bed12 +escherichia_coli_k_12_dh10b-ensembl-eb1,fasta +escherichia_coli_k_12_dh10b-ensembl-eb1,bwa_index +escherichia_coli_k_12_dh10b-ensembl-eb1,bowtie2_index +escherichia_coli_k_12_dh10b-ensembl-eb1,star_index +escherichia_coli_k_12_dh10b-ensembl-eb1,bismark_bt2_index +escherichia_coli_k_12_dh10b-ensembl-eb1,gencode_gtf +escherichia_coli_k_12_dh10b-ensembl-eb1,bed12 +gallus_gallus-ensembl-galgal4,fasta +gallus_gallus-ensembl-galgal4,bwa_index +gallus_gallus-ensembl-galgal4,bowtie2_index +gallus_gallus-ensembl-galgal4,star_index +gallus_gallus-ensembl-galgal4,bismark_bt2_index +gallus_gallus-ensembl-galgal4,gencode_gtf +gallus_gallus-ensembl-galgal4,bed12 +gallus_gallus-ucsc-galgal4,fasta +gallus_gallus-ucsc-galgal4,bwa_index +gallus_gallus-ucsc-galgal4,bowtie2_index +gallus_gallus-ucsc-galgal4,star_index +gallus_gallus-ucsc-galgal4,bismark_bt2_index +gallus_gallus-ucsc-galgal4,gencode_gtf +gallus_gallus-ucsc-galgal4,bed12 +glycine_max-ensembl-gm01,fasta +glycine_max-ensembl-gm01,bwa_index +glycine_max-ensembl-gm01,bowtie2_index +glycine_max-ensembl-gm01,star_index +glycine_max-ensembl-gm01,bismark_bt2_index +glycine_max-ensembl-gm01,gencode_gtf +glycine_max-ensembl-gm01,bed12 +macaca_mulatta-ensembl-mmul1,fasta +macaca_mulatta-ensembl-mmul1,bwa_index +macaca_mulatta-ensembl-mmul1,bowtie2_index +macaca_mulatta-ensembl-mmul1,star_index +macaca_mulatta-ensembl-mmul1,bismark_bt2_index +macaca_mulatta-ensembl-mmul1,gencode_gtf +macaca_mulatta-ensembl-mmul1,bed12 +oryza_sativa_japonica-ensembl-irgsp10,fasta +oryza_sativa_japonica-ensembl-irgsp10,bwa_index +oryza_sativa_japonica-ensembl-irgsp10,bowtie2_index +oryza_sativa_japonica-ensembl-irgsp10,star_index +oryza_sativa_japonica-ensembl-irgsp10,bismark_bt2_index +oryza_sativa_japonica-ensembl-irgsp10,gencode_gtf +oryza_sativa_japonica-ensembl-irgsp10,bed12 +pan_troglodytes-ensembl-chimp214,fasta +pan_troglodytes-ensembl-chimp214,bwa_index +pan_troglodytes-ensembl-chimp214,bowtie2_index +pan_troglodytes-ensembl-chimp214,star_index +pan_troglodytes-ensembl-chimp214,bismark_bt2_index +pan_troglodytes-ensembl-chimp214,gencode_gtf +pan_troglodytes-ensembl-chimp214,bed12 +pan_troglodytes-ucsc-pantro4,fasta +pan_troglodytes-ucsc-pantro4,bwa_index +pan_troglodytes-ucsc-pantro4,bowtie2_index +pan_troglodytes-ucsc-pantro4,star_index +pan_troglodytes-ucsc-pantro4,bismark_bt2_index +pan_troglodytes-ucsc-pantro4,gencode_gtf +pan_troglodytes-ucsc-pantro4,bed12 +rattus_norvegicus-ensembl-rnor50,fasta +rattus_norvegicus-ensembl-rnor50,bwa_index +rattus_norvegicus-ensembl-rnor50,bowtie2_index +rattus_norvegicus-ensembl-rnor50,star_index +rattus_norvegicus-ensembl-rnor50,bismark_bt2_index +rattus_norvegicus-ensembl-rnor50,gencode_gtf +rattus_norvegicus-ensembl-rnor50,bed12 +rattus_norvegicus-ensembl-rnor60,fasta +rattus_norvegicus-ensembl-rnor60,bwa_index +rattus_norvegicus-ensembl-rnor60,bowtie2_index +rattus_norvegicus-ensembl-rnor60,star_index +rattus_norvegicus-ensembl-rnor60,bismark_bt2_index +rattus_norvegicus-ensembl-rnor60,gencode_gtf +rattus_norvegicus-ensembl-rnor60,bed12 +rattus_norvegicus-ucsc-rn6,fasta +rattus_norvegicus-ucsc-rn6,bwa_index +rattus_norvegicus-ucsc-rn6,bowtie2_index +rattus_norvegicus-ucsc-rn6,star_index +rattus_norvegicus-ucsc-rn6,bismark_bt2_index +rattus_norvegicus-ucsc-rn6,gencode_gtf +rattus_norvegicus-ucsc-rn6,bed12 +saccharomyces_cerevisiae-ensembl-r6411,fasta +saccharomyces_cerevisiae-ensembl-r6411,bwa_index +saccharomyces_cerevisiae-ensembl-r6411,bowtie2_index +saccharomyces_cerevisiae-ensembl-r6411,star_index +saccharomyces_cerevisiae-ensembl-r6411,bismark_bt2_index +saccharomyces_cerevisiae-ensembl-r6411,gencode_gtf +saccharomyces_cerevisiae-ensembl-r6411,bed12 +saccharomyces_cerevisiae-ucsc-saccer3,fasta +saccharomyces_cerevisiae-ucsc-saccer3,bwa_index +saccharomyces_cerevisiae-ucsc-saccer3,bowtie2_index +saccharomyces_cerevisiae-ucsc-saccer3,star_index +saccharomyces_cerevisiae-ucsc-saccer3,bismark_bt2_index +schizosaccharomyces_pombe-ensembl-ef2,fasta +schizosaccharomyces_pombe-ensembl-ef2,bwa_index +schizosaccharomyces_pombe-ensembl-ef2,bowtie2_index +schizosaccharomyces_pombe-ensembl-ef2,star_index +schizosaccharomyces_pombe-ensembl-ef2,bismark_bt2_index +schizosaccharomyces_pombe-ensembl-ef2,gencode_gtf +schizosaccharomyces_pombe-ensembl-ef2,bed12 +sorghum_bicolor-ensembl-sbi1,fasta +sorghum_bicolor-ensembl-sbi1,bwa_index +sorghum_bicolor-ensembl-sbi1,bowtie2_index +sorghum_bicolor-ensembl-sbi1,star_index +sorghum_bicolor-ensembl-sbi1,bismark_bt2_index +sorghum_bicolor-ensembl-sbi1,gencode_gtf +sorghum_bicolor-ensembl-sbi1,bed12 +sus_scrofa-ensembl-sscrofa102,fasta +sus_scrofa-ensembl-sscrofa102,bwa_index +sus_scrofa-ensembl-sscrofa102,bowtie2_index +sus_scrofa-ensembl-sscrofa102,star_index +sus_scrofa-ensembl-sscrofa102,bismark_bt2_index +sus_scrofa-ensembl-sscrofa102,gencode_gtf +sus_scrofa-ensembl-sscrofa102,bed12 +sus_scrofa-ucsc-susscr3,fasta +sus_scrofa-ucsc-susscr3,bwa_index +sus_scrofa-ucsc-susscr3,bowtie2_index +sus_scrofa-ucsc-susscr3,star_index +sus_scrofa-ucsc-susscr3,bismark_bt2_index +sus_scrofa-ucsc-susscr3,gencode_gtf +sus_scrofa-ucsc-susscr3,bed12 +zea_mays-ensembl-agpv3,fasta +zea_mays-ensembl-agpv3,bwa_index +zea_mays-ensembl-agpv3,bowtie2_index +zea_mays-ensembl-agpv3,star_index +zea_mays-ensembl-agpv3,bismark_bt2_index +zea_mays-ensembl-agpv3,gencode_gtf +zea_mays-ensembl-agpv3,bed12 diff --git a/asset_pep/recipe_inputs.csv b/asset_pep/recipe_inputs.csv index 52bccb5..7339a0f 100644 --- a/asset_pep/recipe_inputs.csv +++ b/asset_pep/recipe_inputs.csv @@ -39,3 +39,232 @@ caenorhabditis_elegans-ucsc-ce10-star_index,star_index,fasta,assets, caenorhabditis_elegans-ucsc-ce10-bismark_bt2_index,bismark_bt2_index,fasta,assets, caenorhabditis_elegans-ucsc-ce10-gencode_gtf,gencode_gtf,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf,files, caenorhabditis_elegans-ucsc-ce10-bed12,bed12,s3://ngi-igenomes/igenomes/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed,files, 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