From b3c2ca7749d4b3bee85ced5e5648f0208da7dcac Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Thu, 11 Jul 2024 14:56:15 +0200 Subject: [PATCH 1/5] add parameters for cellranger mkfastq --- jsons/parameters.json | 90 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 90 insertions(+) diff --git a/jsons/parameters.json b/jsons/parameters.json index 2d8c9a4..44aca0f 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -10585,6 +10585,21 @@ "value_translations": {}, "value_type": "float" }, + { + "default_value": "local", + "description": "Job manager to use. Options are: local (default), a cluster job mode (i.e., sge, lsf, slurm), or the path to a .template file", + "key_translations": { + "cellranger_mkfastq_style_1": "--jobmode", + "ursgal_style_1": "jobmode" + }, + "name": "jobmode", + "tag": [ + "cellranger_mkfastq" + ], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "str" + }, { "default_value": ".u.json", "description": "Exension for .json files", @@ -10955,6 +10970,21 @@ "value_translations": {}, "value_type": "str" }, + { + "default_value": 8, + "description": "max cores the pipeline may request at one time. Only applies to local jobs", + "key_translations": { + "cellranger_mkfastq_style_1": "--localcores", + "ursgal_style_1": "localcores" + }, + "name": "localcores", + "tag": [ + "cellranger_mkfastq" + ], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "int" + }, { "default_value": true, "description": " Generate and use mass difference fragment index in addition to the regular fragment index for search. This allows shifted fragment ions - fragment ions with mass increased by the calculated mass difference, to be included in scoring. ", @@ -11014,6 +11044,21 @@ }, "value_type": "bool" }, + { + "default_value": 57, + "description": "max GB the pipeline may request at one time. Only applies to local jobs", + "key_translations": { + "cellranger_mkfastq_style_1": "--localmem", + "ursgal_style_1": "localmem" + }, + "name": "localmem", + "tag": [ + "cellranger_mkfastq" + ], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "int" + }, { "default_value": 1.0, "description": "Fold change Threshold to narrow down significantly regulated identifiers", @@ -15654,6 +15699,21 @@ }, "value_type": "bool" }, + { + "default_value": "$projectId", + "description": "Custom project name,", + "key_translations": { + "cellranger_mkfastq_style_1": "--project", + "ursgal_style_1": "project" + }, + "name": "project", + "tag": [ + "cellranger_mkfastq" + ], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "str" + }, { "default_value": "heuristic", "description": "Protein inference algorithm to be used.", @@ -16687,6 +16747,21 @@ }, "value_type": "bool" }, + { + "default_value": "", + "description": "Path to the Illumina BCL run folder", + "key_translations": { + "cellranger_mkfastq_style_1": "--run", + "ursgal_style_1": "run" + }, + "name": "run", + "tag": [ + "cellranger_mkfastq" + ], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "str" + }, { "default_value": "None", "description": "This parameter is only relevant for pepXML output and is used solely to annotate additional information in the output. It does not influence the search. The sample enzyme could be different from the search enzyme i.e. the sample enzyme is 'trypsin' yet the search enzyme is 'No-enzyme' for a non-specific search. Hence the need for this separate parameter.Default value is 'None', which is translated to 0.", @@ -16849,6 +16924,21 @@ }, "value_type": "str" }, + { + "default_value": "", + "description": "Path to sample sheet", + "key_translations": { + "cellranger_mkfastq_style_1": "--samplesheet", + "ursgal_style_1": "samplesheet" + }, + "name": "samplesheet", + "tag": [ + "cellranger_mkfastq" + ], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "str" + }, { "default_value": [], "description": "Spectra rejected during mzml2mgf conversion", From 944f91ecde13472eaca9fc36a887559b72a9bfc8 Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Thu, 11 Jul 2024 15:20:33 +0200 Subject: [PATCH 2/5] add style --- jsons/styles.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/jsons/styles.json b/jsons/styles.json index c2eba52..dce3e11 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -15,6 +15,14 @@ "1.3.1" ] }, + { + "name": "Cellranger mkfastq", + "reference": "Zheng, G. X. Y. et al. (2017). Massively parallel digital transcriptional profiling of single cells. Nature Communications 8: 1-12, doi:10.1038/ncomms14049", + "style": "cellranger_mkfastq_style_1", + "versions": [ + "1.0.0" + ] + }, { "name": "Combine PEP", "reference": "Combines PEP scores from different search engines.", From 95a35eafdbe92354d622886cb912d8d2bfd4a478 Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Thu, 11 Jul 2024 17:50:35 +0200 Subject: [PATCH 3/5] fix params that were already there --- jsons/parameters.json | 50 ++++++++++++++++--------------------------- 1 file changed, 18 insertions(+), 32 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index 44aca0f..d8fa80c 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -4162,6 +4162,7 @@ "align_files_dbscan_style_1": "n_jobs", "align_scans_dbscan_style_1": "n_jobs", "bowtie_style_1": "-p", + "cellranger_mkfastq_style_1": "--localcores", "comet_style_1": "num_threads", "cutadapt_style_1": "-j", "diann_library_empirical_style_1": "--threads", @@ -4207,6 +4208,12 @@ -1 ] ], + "cellranger_mkfastq_style_1": [ + [ + -1, + 8 + ] + ], "comet_style_1": [ [ -1, @@ -10970,21 +10977,6 @@ "value_translations": {}, "value_type": "str" }, - { - "default_value": 8, - "description": "max cores the pipeline may request at one time. Only applies to local jobs", - "key_translations": { - "cellranger_mkfastq_style_1": "--localcores", - "ursgal_style_1": "localcores" - }, - "name": "localcores", - "tag": [ - "cellranger_mkfastq" - ], - "triggers_rerun": true, - "value_translations": {}, - "value_type": "int" - }, { "default_value": true, "description": " Generate and use mass difference fragment index in addition to the regular fragment index for search. This allows shifted fragment ions - fragment ions with mass increased by the calculated mass difference, to be included in scoring. ", @@ -11044,21 +11036,6 @@ }, "value_type": "bool" }, - { - "default_value": 57, - "description": "max GB the pipeline may request at one time. Only applies to local jobs", - "key_translations": { - "cellranger_mkfastq_style_1": "--localmem", - "ursgal_style_1": "localmem" - }, - "name": "localmem", - "tag": [ - "cellranger_mkfastq" - ], - "triggers_rerun": true, - "value_translations": {}, - "value_type": "int" - }, { "default_value": 1.0, "description": "Fold change Threshold to narrow down significantly regulated identifiers", @@ -11902,6 +11879,7 @@ "default_value": 31000000000, "description": "Maximum bytes of allowed RAM usage.", "key_translations": { + "cellranger_mkfastq_style_1": "--localmem", "star_index_style_1": "--limitGenomeGenerateRAM", "ursgal_style_1": "max_ram" }, @@ -11910,7 +11888,14 @@ "configuration" ], "triggers_rerun": false, - "value_translations": {}, + "value_translations": { + "cellranger_mkfastq_style_1": [ + [ + 31000000000, + 57 + ] + ] + }, "value_type": "int" }, { @@ -16756,7 +16741,8 @@ }, "name": "run", "tag": [ - "cellranger_mkfastq" + "cellranger_mkfastq", + "input_file" ], "triggers_rerun": true, "value_translations": {}, From a9a88c2731b0e52c627cb937e6626ee09cba8828 Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Wed, 17 Jul 2024 14:24:32 +0200 Subject: [PATCH 4/5] cellranger param adjusted --- jsons/parameters.json | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index d8fa80c..c476eda 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -4162,7 +4162,7 @@ "align_files_dbscan_style_1": "n_jobs", "align_scans_dbscan_style_1": "n_jobs", "bowtie_style_1": "-p", - "cellranger_mkfastq_style_1": "--localcores", + "cellranger_style_1": "--localcores", "comet_style_1": "num_threads", "cutadapt_style_1": "-j", "diann_library_empirical_style_1": "--threads", @@ -4208,7 +4208,7 @@ -1 ] ], - "cellranger_mkfastq_style_1": [ + "cellranger_style_1": [ [ -1, 8 @@ -10596,7 +10596,7 @@ "default_value": "local", "description": "Job manager to use. Options are: local (default), a cluster job mode (i.e., sge, lsf, slurm), or the path to a .template file", "key_translations": { - "cellranger_mkfastq_style_1": "--jobmode", + "cellranger_style_1": "--jobmode", "ursgal_style_1": "jobmode" }, "name": "jobmode", @@ -11879,7 +11879,7 @@ "default_value": 31000000000, "description": "Maximum bytes of allowed RAM usage.", "key_translations": { - "cellranger_mkfastq_style_1": "--localmem", + "cellranger_style_1": "--localmem", "star_index_style_1": "--limitGenomeGenerateRAM", "ursgal_style_1": "max_ram" }, @@ -11889,7 +11889,7 @@ ], "triggers_rerun": false, "value_translations": { - "cellranger_mkfastq_style_1": [ + "cellranger_style_1": [ [ 31000000000, 57 @@ -15688,7 +15688,7 @@ "default_value": "$projectId", "description": "Custom project name,", "key_translations": { - "cellranger_mkfastq_style_1": "--project", + "cellranger_style_1": "--project", "ursgal_style_1": "project" }, "name": "project", @@ -16736,7 +16736,7 @@ "default_value": "", "description": "Path to the Illumina BCL run folder", "key_translations": { - "cellranger_mkfastq_style_1": "--run", + "cellranger_style_1": "--run", "ursgal_style_1": "run" }, "name": "run", @@ -16914,7 +16914,7 @@ "default_value": "", "description": "Path to sample sheet", "key_translations": { - "cellranger_mkfastq_style_1": "--samplesheet", + "cellranger_style_1": "--samplesheet", "ursgal_style_1": "samplesheet" }, "name": "samplesheet", From 3e5009410ecd936ac9060e590365cda3017ed165 Mon Sep 17 00:00:00 2001 From: vgp57214_gsk Date: Thu, 18 Jul 2024 12:17:50 +0200 Subject: [PATCH 5/5] fix style --- jsons/parameters.json | 19 ++++++------------- jsons/styles.json | 4 ++-- 2 files changed, 8 insertions(+), 15 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index c476eda..61a3227 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -4211,7 +4211,7 @@ "cellranger_style_1": [ [ -1, - 8 + 2 ] ], "comet_style_1": [ @@ -10600,9 +10600,7 @@ "ursgal_style_1": "jobmode" }, "name": "jobmode", - "tag": [ - "cellranger_mkfastq" - ], + "tag": ["transcriptomics", "cellranger"], "triggers_rerun": true, "value_translations": {}, "value_type": "str" @@ -11892,7 +11890,7 @@ "cellranger_style_1": [ [ 31000000000, - 57 + 4 ] ] }, @@ -15693,7 +15691,7 @@ }, "name": "project", "tag": [ - "cellranger_mkfastq" + "transcriptomics", "cellranger" ], "triggers_rerun": true, "value_translations": {}, @@ -16740,10 +16738,7 @@ "ursgal_style_1": "run" }, "name": "run", - "tag": [ - "cellranger_mkfastq", - "input_file" - ], + "tag": ["transcriptomics", "cellranger"], "triggers_rerun": true, "value_translations": {}, "value_type": "str" @@ -16918,9 +16913,7 @@ "ursgal_style_1": "samplesheet" }, "name": "samplesheet", - "tag": [ - "cellranger_mkfastq" - ], + "tag": ["transcriptomics", "cellranger"], "triggers_rerun": true, "value_translations": {}, "value_type": "str" diff --git a/jsons/styles.json b/jsons/styles.json index dce3e11..b4af379 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -18,9 +18,9 @@ { "name": "Cellranger mkfastq", "reference": "Zheng, G. X. Y. et al. (2017). Massively parallel digital transcriptional profiling of single cells. Nature Communications 8: 1-12, doi:10.1038/ncomms14049", - "style": "cellranger_mkfastq_style_1", + "style": "cellranger_style_1", "versions": [ - "1.0.0" + "8.0.1" ] }, {