From 9682d42ef4d3430515d01e3ae0763d0ae81d4d57 Mon Sep 17 00:00:00 2001 From: mikaelamo Date: Mon, 31 Jul 2023 13:34:38 +0200 Subject: [PATCH 1/5] Adding organise runfolder yml. --- config/organise_runfolder.yml | 43 +++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 config/organise_runfolder.yml diff --git a/config/organise_runfolder.yml b/config/organise_runfolder.yml new file mode 100644 index 0000000..bdadcfc --- /dev/null +++ b/config/organise_runfolder.yml @@ -0,0 +1,43 @@ +--- +#Input: runfolder_name + +#Currently named runfolderpath and runfolder to harmonize with rnaseq config by Monika, but for specific runfolder delivery, technically, these could be "merged" to one. +runfolderpath: /proj/ngi2016001/incoming +runfolder: / +organised: /Projects/ + +#current path is /proj/ngi2016001/incoming//Projects/// +#The following is based on that we are to keep the same directory structure as above. +files_to_organize: + + #The fastq files + - source: /Unaligned/* + destination: /(?P=projectid)//Sample_(?P=samplename)/ + options: + required: True + symlink: True + regexp: (?P[\w-]+)/Sample_(?P[\w-]+)/(?P=samplename)_S(?P\d+)_L(?P\d+)_R(?P\d)_001.fastq.gz + + #The MultiQC files + - source: /seqreports/project/* + destination: /(?P=projectid)// + options: + required: True + symlink: True + regexp: (?P[\w-]+)/(?P\w+)_(?P=projectid)_multiqc_report[\w.-]+ + + + + #what we are lacking, and what might need to be created outside the config is: + #1. checksums.md5 + #2. Encrypted samplesheet + #As far as I know, these don't exist prior to organization. + +# #hypothethical undetermined, needs an input of lane(s) connected to project +# #We will not include this at this point, as it requires additional input. Will maybe end up in its own config or something. +# - source: /Unaligned/Undetermined/Undetermined_S0_L_R_001.fastq.gz +# destination: /Unaligned//Undetermined/ +# options: +# required: False +# symlink: True + From 582bb3d183860f49978d3c77b7809d9ce2aaf91f Mon Sep 17 00:00:00 2001 From: mikaelamo Date: Mon, 31 Jul 2023 13:37:51 +0200 Subject: [PATCH 2/5] Adding organise runfolder yml. --- organise_runfolder.yml | 43 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 organise_runfolder.yml diff --git a/organise_runfolder.yml b/organise_runfolder.yml new file mode 100644 index 0000000..bdadcfc --- /dev/null +++ b/organise_runfolder.yml @@ -0,0 +1,43 @@ +--- +#Input: runfolder_name + +#Currently named runfolderpath and runfolder to harmonize with rnaseq config by Monika, but for specific runfolder delivery, technically, these could be "merged" to one. +runfolderpath: /proj/ngi2016001/incoming +runfolder: / +organised: /Projects/ + +#current path is /proj/ngi2016001/incoming//Projects/// +#The following is based on that we are to keep the same directory structure as above. +files_to_organize: + + #The fastq files + - source: /Unaligned/* + destination: /(?P=projectid)//Sample_(?P=samplename)/ + options: + required: True + symlink: True + regexp: (?P[\w-]+)/Sample_(?P[\w-]+)/(?P=samplename)_S(?P\d+)_L(?P\d+)_R(?P\d)_001.fastq.gz + + #The MultiQC files + - source: /seqreports/project/* + destination: /(?P=projectid)// + options: + required: True + symlink: True + regexp: (?P[\w-]+)/(?P\w+)_(?P=projectid)_multiqc_report[\w.-]+ + + + + #what we are lacking, and what might need to be created outside the config is: + #1. checksums.md5 + #2. Encrypted samplesheet + #As far as I know, these don't exist prior to organization. + +# #hypothethical undetermined, needs an input of lane(s) connected to project +# #We will not include this at this point, as it requires additional input. Will maybe end up in its own config or something. +# - source: /Unaligned/Undetermined/Undetermined_S0_L_R_001.fastq.gz +# destination: /Unaligned//Undetermined/ +# options: +# required: False +# symlink: True + From c5e9423a8c8936487724e533fe45a65d2439c6ca Mon Sep 17 00:00:00 2001 From: mikaelamo Date: Mon, 31 Jul 2023 13:47:30 +0200 Subject: [PATCH 3/5] removed abundant file --- organise_runfolder.yml | 43 ------------------------------------------ 1 file changed, 43 deletions(-) delete mode 100644 organise_runfolder.yml diff --git a/organise_runfolder.yml b/organise_runfolder.yml deleted file mode 100644 index bdadcfc..0000000 --- a/organise_runfolder.yml +++ /dev/null @@ -1,43 +0,0 @@ ---- -#Input: runfolder_name - -#Currently named runfolderpath and runfolder to harmonize with rnaseq config by Monika, but for specific runfolder delivery, technically, these could be "merged" to one. -runfolderpath: /proj/ngi2016001/incoming -runfolder: / -organised: /Projects/ - -#current path is /proj/ngi2016001/incoming//Projects/// -#The following is based on that we are to keep the same directory structure as above. -files_to_organize: - - #The fastq files - - source: /Unaligned/* - destination: /(?P=projectid)//Sample_(?P=samplename)/ - options: - required: True - symlink: True - regexp: (?P[\w-]+)/Sample_(?P[\w-]+)/(?P=samplename)_S(?P\d+)_L(?P\d+)_R(?P\d)_001.fastq.gz - - #The MultiQC files - - source: /seqreports/project/* - destination: /(?P=projectid)// - options: - required: True - symlink: True - regexp: (?P[\w-]+)/(?P\w+)_(?P=projectid)_multiqc_report[\w.-]+ - - - - #what we are lacking, and what might need to be created outside the config is: - #1. checksums.md5 - #2. Encrypted samplesheet - #As far as I know, these don't exist prior to organization. - -# #hypothethical undetermined, needs an input of lane(s) connected to project -# #We will not include this at this point, as it requires additional input. Will maybe end up in its own config or something. -# - source: /Unaligned/Undetermined/Undetermined_S0_L_R_001.fastq.gz -# destination: /Unaligned//Undetermined/ -# options: -# required: False -# symlink: True - From ced43d8118e974124c2964f1f86b00bf70712259 Mon Sep 17 00:00:00 2001 From: mikaelamo Date: Fri, 4 Aug 2023 10:43:04 +0200 Subject: [PATCH 4/5] Changed indentation in organise_runfolder.yml and moved the config to new subdir config/organise_config/ --- config/organise_config/organise_runfolder.yml | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 config/organise_config/organise_runfolder.yml diff --git a/config/organise_config/organise_runfolder.yml b/config/organise_config/organise_runfolder.yml new file mode 100644 index 0000000..78c1cb2 --- /dev/null +++ b/config/organise_config/organise_runfolder.yml @@ -0,0 +1,43 @@ +--- +#Input: runfolder_name + +#Currently named runfolderpath and runfolder to harmonize with rnaseq config by Monika, but for specific runfolder delivery, technically, these could be "merged" to one. +runfolderpath: /proj/ngi2016001/incoming +runfolder: / +organised: /Projects/ + +#current path is /proj/ngi2016001/incoming//Projects/// +#The following is based on that we are to keep the same directory structure as above. +files_to_organize: + + #The fastq files + - source: /Unaligned/* + destination: /(?P=projectid)//Sample_(?P=samplename)/ + options: + required: True + symlink: True + regexp: (?P[\w-]+)/Sample_(?P[\w-]+)/(?P=samplename)_S(?P\d+)_L(?P\d+)_R(?P\d)_001.fastq.gz + + #The MultiQC files + - source: /seqreports/project/* + destination: /(?P=projectid)// + options: + required: True + symlink: True + regexp: (?P[\w-]+)/(?P\w+)_(?P=projectid)_multiqc_report[\w.-]+ + + + +#what we are lacking, and what might need to be created outside the config is: +#1. checksums.md5 +#2. Encrypted samplesheet +#As far as I know, these don't exist prior to organization. + +# #hypothethical undetermined, needs an input of lane(s) connected to project +# #We will not include this at this point, as it requires additional input. Will maybe end up in its own config or something. +# - source: /Unaligned/Undetermined/Undetermined_S0_L_R_001.fastq.gz +# destination: /Unaligned//Undetermined/ +# options: +# required: False +# symlink: True + From b68e85563723455ca78129b220ed833047503a09 Mon Sep 17 00:00:00 2001 From: mikaelamo Date: Fri, 4 Aug 2023 13:20:50 +0200 Subject: [PATCH 5/5] Removed forgotten file --- config/organise_runfolder.yml | 43 ----------------------------------- 1 file changed, 43 deletions(-) delete mode 100644 config/organise_runfolder.yml diff --git a/config/organise_runfolder.yml b/config/organise_runfolder.yml deleted file mode 100644 index bdadcfc..0000000 --- a/config/organise_runfolder.yml +++ /dev/null @@ -1,43 +0,0 @@ ---- -#Input: runfolder_name - -#Currently named runfolderpath and runfolder to harmonize with rnaseq config by Monika, but for specific runfolder delivery, technically, these could be "merged" to one. -runfolderpath: /proj/ngi2016001/incoming -runfolder: / -organised: /Projects/ - -#current path is /proj/ngi2016001/incoming//Projects/// -#The following is based on that we are to keep the same directory structure as above. -files_to_organize: - - #The fastq files - - source: /Unaligned/* - destination: /(?P=projectid)//Sample_(?P=samplename)/ - options: - required: True - symlink: True - regexp: (?P[\w-]+)/Sample_(?P[\w-]+)/(?P=samplename)_S(?P\d+)_L(?P\d+)_R(?P\d)_001.fastq.gz - - #The MultiQC files - - source: /seqreports/project/* - destination: /(?P=projectid)// - options: - required: True - symlink: True - regexp: (?P[\w-]+)/(?P\w+)_(?P=projectid)_multiqc_report[\w.-]+ - - - - #what we are lacking, and what might need to be created outside the config is: - #1. checksums.md5 - #2. Encrypted samplesheet - #As far as I know, these don't exist prior to organization. - -# #hypothethical undetermined, needs an input of lane(s) connected to project -# #We will not include this at this point, as it requires additional input. Will maybe end up in its own config or something. -# - source: /Unaligned/Undetermined/Undetermined_S0_L_R_001.fastq.gz -# destination: /Unaligned//Undetermined/ -# options: -# required: False -# symlink: True -