diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c8f360e..45c758c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -21,3 +21,6 @@ jobs: - name: Launch tests run: | nosetests ./tests + - name: Lint config files + run: | + yamllint -c .yamllint.yml config/organise_configs/*.yml diff --git a/.yammlint.yml b/.yammlint.yml new file mode 100644 index 0000000..ae48435 --- /dev/null +++ b/.yammlint.yml @@ -0,0 +1,6 @@ +extends: default + +rules: + line-length: + max: 80 + level: warning diff --git a/config/organise_configs/runfolder.yml b/config/organise_configs/runfolder.yml index c342532..1aed488 100644 --- a/config/organise_configs/runfolder.yml +++ b/config/organise_configs/runfolder.yml @@ -1,44 +1,46 @@ --- -#Input: runfolder_name +# 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. +# Currently named runfolderpath and runfolder to harmonize with rnaseq config +# by Monika, but for specific runfolder delivery, technically, these could be +# "merged" to one. variables: runfolderpath: /proj/ngi2016001/incoming runfolder: "{runfolderpath}/{runfolder_name}" organised: "{runfolder}/Projects/" -#current path is /proj/ngi2016001/incoming//Projects/// -#The following is based on that we are to keep the same directory structure as above. +# 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 + # The fastq files - source: "{runfolder}/Unaligned/*" destination: "{organised}/{projectid}/{runfolder_name}/Sample_{samplename}/" options: - required: True + required: true link_type: softlink - regex: (?P[\w-]+)/Sample_(?P[\w-]+)/(?P=samplename)_S(?P\d+)_L(?P\d+)_R(?P\d)_001.fastq.gz + regex: (?P[\w-]+)/Sample_(?P[\w-]+)/(?P=samplename)_S(?P\d+)_L(?P\d+)_R(?P\d)_001.fastq.gz # yamllint disable-line - # The MultiQC files + # The MultiQC files - source: "{runfolder}/seqreports/project/*" destination: "{organised}/{projectid}//" options: - required: True + required: true link_type: softlink regexp: (?P[\w-]+)/\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. - -#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. +# 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 - diff --git a/requirements/dev b/requirements/dev index 77da1a7..6f96eec 100644 --- a/requirements/dev +++ b/requirements/dev @@ -1,4 +1,4 @@ -r prod mock==4.0.3 nose==1.3.7 - +yamllint==1.32.0