cbi-star
commented
1 year ago In the created hifiasm/tasks folders, there are several major changes/additions. (1) the hfiasm-related wdl-files are modified and moved here; (2) sample_hifiasm.cohort.wdl created/modified to deal with sample-level hifiasm; (3) trio_hifiasm.cohort.wdl created/modified to deal with trio-level hifiasm; (4) triobev.wdl created to test with yak triobin/trioeval independently; (5) yak.wdl uses additional input data, trial.parents_list, to make yak-calculation easy. More details here: https://github.com/cbi-star/pb-human-wgs-workflow-wdl/commit/ef14de3eef4ecd58f6c03160d2a9dcce0ec7f938
The restructured pipeline in this repo is called now as automatic genome-sequence analysis pipeline or agape for short, presented the following major changes based on the main repo:
Use a unified data structure as input and re-designed workflows to restructure the wdl-pipeline in hope to simplify the wdl-scripts and provide easy maintenance. There are several major changes. (1) unifying affected/unaffected into one-line code using new input data structure in all wdl-file if applied; (2) removing this struct definition: CohortInfo from structs.wdl and replace it with Array[SampleInfo] in the main workflow, and accordingly changed all related wdl-files whenever applied; (3) modified the struct SampleInfo by adding one element: Boolean? affected; (4) run sample-hifiasm and trio-hifiasm both in the main workflow: trial.wdl; (5) run a separate fasta-conversion once for all, and thus a new workflow created under process.smrtcells: fasta_conversion.wdl, which are used by jellyfish, sample and trio-hifiasm; (6) created new folders (hifiasm/tasks) and new wdl-files to deal with hifiasm computing independently, and to put related workflows/tasks (re-written/modified) into this folders; (7) change all import links to include /cbi-star/ for each wdl-files whenever applied. See details here: https://github.com/cbi-star/pb-human-wgs-workflow-wdl/commit/f8c4248df9227964dbe93762581d6732383dfdc5
(8) In order to reduce task callings, the separate sub-workflow separate_data_and_index_files.wdl being removed from the agape WDL-pipeline, and for those workflows calling this sub-workflow: (a) replace it with a local scatter-loop, or (b) when the datafile and indexfile are available from their upstream tasks, simply delete the separate sub-workflow calling and use them. Details can be seen here: https://github.com/cbi-star/pb-human-wgs-workflow-wdl/commit/05a0366f90c2a9608d0d3d66aa1f37e68fc7ccb3
(9) hifiasm.wdl is simplified to reduce the task callings and loading times of docker_image. Three tasks n their sequential callings (gfa2fa, fa2bgzip and bgzip2asm) are merged into one new task/definition. Five different kinds of gfa-files are packed in an array to call as in a scatter-gather loop. Two new workflows are added: gfa2asm.wdl and gfa_asm_single.wdl. Details are here: https://github.com/cbi-star/pb-human-wgs-workflow-wdl/commit/35e5d35365e49153548261d14cdf8e9184c0f91f