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Created with Raphaël 2.2.020Sep13Jul28Jun272622212019151413128762131May30291917151110926Apr2514131211631Mar14FebREADME.md: add dependencies descriptiontp2tp2README: small description of the softwaremaster tp1master tp1README: rename to README.md for md renderingfix file_handle.py pathv0.1.1v0.1.1start to mv file_handle to a new reposDockerfile: mapping add samtool librariesv0.1.0v0.1.0Dockerfile: quality_control remove doublon of cutadapt installmapping.nf: new syntax for samtools 1.5mapping.config: fix samtools pathDockerfile: mapping add install for samtools 1.5mapping.nf: fix bug on mapper binary testquality_control_test.sh: add profile configurationmapping.nf: fix kallisto binary testmapping_test.sh: add profile type configurationnextflow.config: remote sge parameter for local computationmapping.nf: cpus parameters compatible with config filemapping_docker_test.sh: compatible with profile based config filequality_control_docker_test.sh: compatible with profile based confignextflow.config: alternative config for alternative profilesnextflow.config: maping.config into a new filenextflow.config: put quality_control.nf config in a separate filenextflow.config: defaut configuration for quality_control.nfquality_control.nf: correction to comply with nextflow.config formatnextflow.config: modify docker default ressourcesnextflow.config: add quality_control.nf and mapping.nf optionsmapping_test.sh: uses nextflow.config filemapping.nf: fix HTseq-count pathtests files: add '&& \' at the end of each commandsDockerfile: mapping install htseqmapping.nf: fix samtools to be compatible with many version in sortinggit subrepo clone gitlab_lbmc:jclaud01/tiny_dataset.git data/examples/tiny_dataset/mapping.nf: replace gzip with global gzip variable in indexing processDockerfile: mapping add libtbb2 dependencymapping_docker_test.sh: full suite of tests of mapping.nf in dockermapping.nf: fix split_ref file handelingmapping.nf: fix file handling in get_file_name_annotationmapping.nf: fix file handeling of get_file_name_reference processinit.sh: add docker sectionbioinformatic_pipeline.md: documentation to test the quality_control.nf pipelineDockerfile: mapping.nf install bedtools and samtools