[ { "id": "process_shortreadstags", "name": "process_shortreadstags", "article": "10.1111\/mec.15253", "website": "http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/process_shortreads..php", "git": "", "description": "Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.", "version": "2.64", "documentation": "http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/process_shortreads.php", "multiqc": "custom", "commands": [ { "name": "process_shortreadstags_SE", "cname": "Process shortreadsTags SE", "command": "process_shortreads", "category": "stacks", "output_dir": "process_shortreadstags\/SE", "inputs": [ { "name": "reads_dir", "type": "SE_read_dir", "description": "Directory containing one or more multiplexed read files to process" }, { "name": "tags", "type": "tsv", "description": "Barcode file" } ], "outputs": [ { "name": "reads_demultiplexed", "type": "fq.gz", "file": "{individu}.fastq.gz", "description": "Files of reads for each individual" }, { "name": "read_dir", "type": "SE_read_dir", "file": "\/", "description": "dir containing demultiplexed files" } ], "options": [ { "name": "process_shortreadstags_barcode_type", "type": "select", "choices": [ { "--inline_null": "--inline_null" }, { "--index_null": "--index_null" }, { "--inline_inline": "--inline_inline" }, { "--index_index": "--index_index" }, { "--inline_index": "--inline_index" }, { "--index_inline": "--index_inline" } ], "value": "--inline_null", "label": "Barcode position" }, { "name": "process_shortreadstags_threads", "prefix": "-t", "type": "numeric", "value": 24, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" } ] }, { "name": "process_shortreadstags_PE", "cname": "Process shortreadsTags PE", "command": "process_shortreads", "category": "stacks", "output_dir": "process_shortreadstags\/PE", "inputs": [ { "name": "reads_dir", "type": "PE_read_dir", "description": "Directory containing one or more multiplexed read files to process" }, { "name": "tags", "type": "tsv", "description": "Barcode file" } ], "outputs": [ { "name": "reads_forward_demultiplexed", "type": "fq.gz", "file": "{individu}_R1.fastq.gz", "description": "Files of forward reads for each individual" }, { "name": "reads_reverse_demultiplexed", "type": "fq.gz", "file": "{individu}_R2.fastq.gz", "description": "Files of reverse reads for each individual" }, { "name": "read_dir", "type": "PE_read_dir", "file": "\/", "description": "dir containing demultiplexed files" } ], "options": [ { "name": "process_shortreadstags_barcode_type", "type": "select", "choices": [ { "--inline_null": "--inline_null" }, { "--index_null": "--index_null" }, { "--inline_inline": "--inline_inline" }, { "--index_index": "--index_index" }, { "--inline_index": "--inline_index" }, { "--index_inline": "--index_inline" } ], "value": "--inline_null", "label": "Barcode position" }, { "name": "process_shortreadstags_threads", "prefix": "-t", "type": "numeric", "value": 24, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" } ] } ], "install": [], "citations": { "stacks": [ "Rochette, NC, Rivera-Col\u00f3n, AG, Catchen, JM. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol Ecol. 2019; 28: 4737- 4754. https:\/\/doi.org\/10.1111\/mec.15253" ] }, "yaml": "{\n id: process_shortreadstags,\n name: process_shortreadstags,\n article: 10.1111\/mec.15253,\n website: \"http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/process_shortreads..php\",\n git: \"\",\n description: \"Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.\",\n version: \"2.64\",\n documentation: \"http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/process_shortreads.php\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: process_shortreadstags_SE,\n cname: \"Process shortreadsTags SE\",\n command: process_shortreads,\n category: \"stacks\",\n output_dir: process_shortreadstags\/SE,\n inputs: \n [\n { name: \"reads_dir\", type: \"SE_read_dir\", description: \"Directory containing one or more multiplexed read files to process\" },\n { name: tags, type: \"tsv\", description: \"Barcode file\" }\n ],\n outputs:\n [\n { name: reads_demultiplexed, type: \"fq.gz\", file: \"{individu}.fastq.gz\", description: \"Files of reads for each individual\" },\n { name: read_dir, type: \"SE_read_dir\", file: \"\/\", description: \"dir containing demultiplexed files\"}\n ],\n options:\n [\n {\n name: process_shortreadstags_barcode_type,\n type: select,\n choices: [\n --inline_null: \"--inline_null\",\n --index_null: \"--index_null\",\n --inline_inline: \"--inline_inline\",\n --index_index: \"--index_index\",\n --inline_index: \"--inline_index\",\n --index_inline: \"--index_inline\",\n ],\n value: \"--inline_null\",\n label: Barcode position\n },\n {\n name: process_shortreadstags_threads,\n prefix: -t,\n type: numeric,\n value: 24,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n ],\n },\n {\n name: process_shortreadstags_PE,\n cname: \"Process shortreadsTags PE\",\n command: process_shortreads,\n category: \"stacks\",\n output_dir: process_shortreadstags\/PE,\n inputs: \n [\n { name: \"reads_dir\", type: \"PE_read_dir\", description: \"Directory containing one or more multiplexed read files to process\" },\n { name: tags, type: \"tsv\", description: \"Barcode file\" }\n ],\n outputs:\n [\n { name: reads_forward_demultiplexed, type: \"fq.gz\", file: \"{individu}_R1.fastq.gz\", description: \"Files of forward reads for each individual\" },\n { name: reads_reverse_demultiplexed, type: \"fq.gz\", file: \"{individu}_R2.fastq.gz\", description: \"Files of reverse reads for each individual\" },\n { name: read_dir, type: \"PE_read_dir\", file: \"\/\", description: \"dir containing demultiplexed files\"}\n ],\n options:\n [\n {\n name: process_shortreadstags_barcode_type,\n type: select,\n choices: [\n --inline_null: \"--inline_null\",\n --index_null: \"--index_null\",\n --inline_inline: \"--inline_inline\",\n --index_index: \"--index_index\",\n --inline_index: \"--inline_index\",\n --index_inline: \"--index_inline\",\n ],\n value: \"--inline_null\",\n label: Barcode position\n },\n {\n name: process_shortreadstags_threads,\n prefix: -t,\n type: numeric,\n value: 24,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n \n ],\n },\n ],\n install:\n {\n # stacks: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/catchenlab.life.illinois.edu\/stacks\/source\/stacks-2.61.tar.gz \",\n # \"tar -zxvf stacks-2.61.tar.gz\",\n # \"cd stacks-2.61\/\",\n # \".\/configure\",\n # \"make -j 10\",\n # \"make install\",\n # \"mv -t ..\/bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks phasedstacks cstacks process_shortreadstags\",\n # \"cd .. && rm -r stacks-2.61 stacks-2.61.tar.gz\"\n # ]\n },\n citations: {\n stacks: [\n \"Rochette, NC, Rivera-Col\u00f3n, AG, Catchen, JM. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol Ecol. 2019; 28: 4737- 4754. https:\/\/doi.org\/10.1111\/mec.15253\"\n ]\n }\n}\n" } ]