Skip to content

Instantly share code, notes, and snippets.

@mvdbeek
Created October 7, 2015 12:53
Show Gist options
  • Save mvdbeek/687dff5be528b8ec3882 to your computer and use it in GitHub Desktop.
Save mvdbeek/687dff5be528b8ec3882 to your computer and use it in GitHub Desktop.
broken workflow import
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "ChIP-seq analysis",
"steps": {
"0": {
"annotation": "",
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "Input fastq file"
}
],
"name": "Input dataset",
"outputs": [],
"position": {
"left": 168.64338684082031,
"top": 279.14451217651367
},
"tool_errors": null,
"tool_id": null,
"tool_state": "{\"name\": \"Input fastq file\"}",
"tool_version": null,
"type": "data_input",
"user_outputs": []
},
"1": {
"annotation": "Quality check",
"id": 1,
"input_connections": {
"input_file": {
"id": 0,
"output_name": "output"
}
},
"inputs": [],
"name": "Fastqc: Fastqc QC",
"outputs": [
{
"name": "html_file",
"type": "html"
}
],
"position": {
"left": 382.63081359863281,
"top": 176.6435661315918
},
"post_job_actions": {
"HideDatasetActionhtml_file": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "html_file"
}
},
"tool_errors": null,
"tool_id": "fastqc",
"tool_state": "{\"__page__\": 0, \"contaminants\": \"null\", \"out_prefix\": \"\\\"FastQC\\\"\", \"input_file\": \"null\"}",
"tool_version": "0.1",
"type": "tool",
"user_outputs": []
},
"2": {
"annotation": "Map reads to genome",
"id": 2,
"input_connections": {
"singlePaired|sInput1": {
"id": 0,
"output_name": "output"
}
},
"inputs": [],
"name": "Map with Bowtie for Illumina",
"outputs": [
{
"name": "output",
"type": "sam"
},
{
"name": "output_suppressed_reads_l",
"type": "fastq"
},
{
"name": "output_suppressed_reads_r",
"type": "fastq"
},
{
"name": "output_unmapped_reads_l",
"type": "fastq"
},
{
"name": "output_unmapped_reads_r",
"type": "fastq"
}
],
"position": {
"left": 388.63679504394531,
"top": 361.14057540893555
},
"post_job_actions": {
"HideDatasetActionoutput": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output"
},
"HideDatasetActionoutput_suppressed_reads_l": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_suppressed_reads_l"
},
"HideDatasetActionoutput_suppressed_reads_r": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_suppressed_reads_r"
},
"HideDatasetActionoutput_unmapped_reads_l": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_unmapped_reads_l"
},
"HideDatasetActionoutput_unmapped_reads_r": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_unmapped_reads_r"
}
},
"tool_errors": null,
"tool_id": "bowtie_wrapper",
"tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"chromInfo\": \"\\\"/bioinfo/http/prod/hosted/nebula.curie.fr/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sSuppressAlign\\\": \\\"-1\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSeed\\\": \\\"-1\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sMaqSoapAlign\\\": \\\"-1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sTryHard\\\": \\\"noTryHard\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"snMaxBacktracks\\\": \\\"125\\\", \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeedLen\\\": \\\"28\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"sMaxFile\\\": \\\"False\\\"}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}",
"tool_version": "1.1.2",
"type": "tool",
"user_outputs": []
},
"3": {
"annotation": "Convert SAM to BAM",
"id": 3,
"input_connections": {
"source|input1": {
"id": 2,
"output_name": "output"
}
},
"inputs": [],
"name": "SAM-to-BAM",
"outputs": [
{
"name": "output1",
"type": "bam"
}
],
"position": {
"left": 701.62950134277344,
"top": 442.12778854370117
},
"post_job_actions": {
"HideDatasetActionoutput1": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output1"
}
},
"tool_errors": null,
"tool_id": "sam_to_bam",
"tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/bioinfo/http/prod/hosted/nebula.curie.fr/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"name\": \"\\\"BAM_file\\\"\", \"__page__\": 0}",
"tool_version": "1.1.2",
"type": "tool",
"user_outputs": []
},
"4": {
"annotation": "Peak calling",
"id": 4,
"input_connections": {
"input_type|input_chipseq_file1": {
"id": 3,
"output_name": "output1"
}
},
"inputs": [],
"name": "MACS",
"outputs": [
{
"name": "output_bed_file",
"type": "bed"
},
{
"name": "output_xls_to_interval_peaks_file",
"type": "interval"
},
{
"name": "output_xls_to_interval_negative_peaks_file",
"type": "interval"
},
{
"name": "output_treatment_wig_file",
"type": "wig"
},
{
"name": "output_control_wig_file",
"type": "wig"
},
{
"name": "output_extra_files",
"type": "html"
}
],
"position": {
"left": 914.53471374511719,
"top": 353.98197555541992
},
"post_job_actions": {
"HideDatasetActionoutput_bed_file": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_bed_file"
},
"HideDatasetActionoutput_control_wig_file": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_control_wig_file"
},
"HideDatasetActionoutput_extra_files": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_extra_files"
},
"HideDatasetActionoutput_treatment_wig_file": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_treatment_wig_file"
},
"HideDatasetActionoutput_xls_to_interval_negative_peaks_file": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_xls_to_interval_negative_peaks_file"
},
"HideDatasetActionoutput_xls_to_interval_peaks_file": {
"action_arguments": {},
"action_type": "HideDatasetAction",
"output_name": "output_xls_to_interval_peaks_file"
}
},
"tool_errors": null,
"tool_id": "peakcalling_macs",
"tool_state": "{\"gsize\": \"\\\"2700000000.0\\\"\", \"tsize\": \"\\\"25\\\"\", \"futurefdr\": \"\\\"\\\"\", \"__page__\": 0, \"diag_type\": \"{\\\"diag_type_selector\\\": \\\"no_diag\\\", \\\"__current_case__\\\": 1}\", \"input_type\": \"{\\\"input_control_file1\\\": null, \\\"input_chipseq_file1\\\": null, \\\"input_type_selector\\\": \\\"single_end\\\", \\\"__current_case__\\\": 1}\", \"wig_type\": \"{\\\"wig_type_selector\\\": \\\"no_wig\\\", \\\"__current_case__\\\": 1}\", \"nolambda\": \"\\\"False\\\"\", \"experiment_name\": \"\\\"MACS in Galaxy without wiggle without report\\\"\", \"bw\": \"\\\"300\\\"\", \"xls_to_interval\": \"\\\"False\\\"\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"nomodel\\\", \\\"shiftsize\\\": \\\"100\\\", \\\"__current_case__\\\": 0}\", \"mfold\": \"\\\"10,30\\\"\", \"chromInfo\": \"\\\"/bioinfo/http/prod/hosted/nebula.curie.fr/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"pvalue\": \"\\\"1e-05\\\"\"}",
"tool_version": "1.0.1",
"type": "tool",
"user_outputs": []
},
"5": {
"annotation": "",
"id": 5,
"input_connections": {
"inputfile": {
"id": 4,
"output_name": "output_bed_file"
}
},
"inputs": [],
"name": "Get peak distribution around TSS (Transcription factors)",
"outputs": [
{
"name": "outputPNG",
"type": "png"
},
{
"name": "outputPDF",
"type": "pdf"
},
{
"name": "stats",
"type": "tabular"
}
],
"position": {
"left": 1220.6562957763672,
"top": 258.14695358276367
},
"post_job_actions": {},
"tool_errors": null,
"tool_id": "makeTSSdist",
"tool_state": "{\"input_organism\": \"{\\\"version\\\": \\\"hg19\\\", \\\"input_organism_selector\\\": \\\"Human\\\", \\\"__current_case__\\\": 0}\", \"right\": \"\\\"50000\\\"\", \"use_reg\": \"{\\\"use_reg_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"if_PDF\": \"\\\"True\\\"\", \"use_control\": \"{\\\"use_control_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"left\": \"\\\"1000\\\"\", \"chromInfo\": \"\\\"/bioinfo/http/prod/hosted/nebula.curie.fr/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"inputfile\": \"null\"}",
"tool_version": "1.0",
"type": "tool",
"user_outputs": []
},
"6": {
"annotation": "",
"id": 6,
"input_connections": {
"inputfile": {
"id": 4,
"output_name": "output_bed_file"
}
},
"inputs": [],
"name": "Annotation of genes with ChIP-seq peaks (transcription factors)",
"outputs": [
{
"name": "outputPNG",
"type": "png"
},
{
"name": "outputPDF",
"type": "pdf"
},
{
"name": "stats",
"type": "tabular"
},
{
"name": "log",
"type": "tabular"
},
{
"name": "statsControl",
"type": "tabular"
}
],
"position": {
"left": 1256.6219940185547,
"top": 452.1456413269043
},
"post_job_actions": {},
"tool_errors": null,
"tool_id": "annotateGenes",
"tool_state": "{\"input_organism\": \"{\\\"version\\\": \\\"hg19\\\", \\\"input_organism_selector\\\": \\\"Human\\\", \\\"__current_case__\\\": 0}\", \"right\": \"\\\"2000\\\"\", \"use_reg\": \"{\\\"use_reg_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"EnhLeft\": \"\\\"-30000\\\"\", \"if_PDF\": \"\\\"True\\\"\", \"left\": \"\\\"-2000\\\"\", \"use_control\": \"{\\\"use_control_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"DownGene\": \"\\\"5000\\\"\", \"chromInfo\": \"\\\"/bioinfo/http/prod/hosted/nebula.curie.fr/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"inputfile\": \"null\"}",
"tool_version": "1.0",
"type": "tool",
"user_outputs": []
},
"7": {
"annotation": "",
"id": 7,
"input_connections": {
"inputfile": {
"id": 4,
"output_name": "output_bed_file"
}
},
"inputs": [],
"name": "Genomic annotation of Chip-Seq peaks",
"outputs": [
{
"name": "outputPNG",
"type": "png"
},
{
"name": "outputPDF",
"type": "pdf"
},
{
"name": "stats",
"type": "tabular"
},
{
"name": "log",
"type": "tabular"
},
{
"name": "statsControl",
"type": "tabular"
}
],
"position": {
"left": 1247.6363983154297,
"top": 693.1366081237793
},
"post_job_actions": {},
"tool_errors": null,
"tool_id": "annotatePeaks",
"tool_state": "{\"input_organism\": \"{\\\"version\\\": \\\"hg19\\\", \\\"input_organism_selector\\\": \\\"Human\\\", \\\"__current_case__\\\": 0}\", \"right\": \"\\\"2000\\\"\", \"use_reg\": \"{\\\"use_reg_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"minScore\": \"\\\"0.0\\\"\", \"EnhLeft\": \"\\\"-30000\\\"\", \"if_PDF\": \"\\\"False\\\"\", \"left\": \"\\\"-2000\\\"\", \"use_control\": \"{\\\"use_control_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}\", \"DownGene\": \"\\\"5000\\\"\", \"chromInfo\": \"\\\"/bioinfo/http/prod/hosted/nebula.curie.fr/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len\\\"\", \"inputfile\": \"null\"}",
"tool_version": "1.0",
"type": "tool",
"user_outputs": []
}
}
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment