Metagenomics Remove Human Reads#93
Open
kieranmbrown wants to merge 33 commits intonasa:DEV_Metagenomics_rmHR_NF_conversionfrom
Open
Metagenomics Remove Human Reads#93kieranmbrown wants to merge 33 commits intonasa:DEV_Metagenomics_rmHR_NF_conversionfrom
kieranmbrown wants to merge 33 commits intonasa:DEV_Metagenomics_rmHR_NF_conversionfrom
Conversation
would appreciate input on this!
…ow_Documentation/NF_MGEstHostReads-B/Estimate_Host_Reads.config to Metagenomics/Estimate_host_reads_in_raw_data/Workflow_Documentation/NF_MGEstHostReads-B/workflow_code/Estimate_Host_Reads.config
…ation/NF_MGEstHostReads-B/Estimate_Host_Reads.nf to Metagenomics/Estimate_host_reads_in_raw_data/Workflow_Documentation/NF_MGEstHostReads-B/workflow_code/Estimate_Host_Reads.nf
…ow_Documentation/NF_MGEstHostReads-B/workflow_code/Estimate_Host_Reads.config to Metagenomics/Estimate_host_reads_in_raw_data/Workflow_Documentation/NF_MGEstHostReads-B/workflow_code/config/Estimate_Host_Reads.config
bnovak32
requested changes
Aug 15, 2024
Contributor
bnovak32
left a comment
bnovak32
left a comment
There was a problem hiding this comment.
Some general comments: the code blocks in the README need to be executable as-is. Ideally, we want users to be able to run the workflow example by copy/paste of the provided code blocks. As currently written, the README attempts to combine the genelab-utils based instructions from the snakemake workflows with the nextflow instructions from the nextflow workflows. Unfortunately, that is redundant/confusing. Pick one or the other. Further comments are in-line on the README, nextflow, and config files.
...n_reads_from_raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/README.md
Outdated
Show resolved
Hide resolved
...n_reads_from_raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/README.md
Outdated
Show resolved
Hide resolved
...n_reads_from_raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/README.md
Outdated
Show resolved
Hide resolved
...n_reads_from_raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/README.md
Outdated
Show resolved
Hide resolved
...n_reads_from_raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/README.md
Outdated
Show resolved
Hide resolved
..._raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/Remove_Human_Reads.nf
Show resolved
Hide resolved
..._raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/Remove_Human_Reads.nf
Show resolved
Hide resolved
..._data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/Remove_Human_reads.config
Show resolved
Hide resolved
..._data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/Remove_Human_reads.config
Outdated
Show resolved
Hide resolved
..._data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/Remove_Human_reads.config
Outdated
Show resolved
Hide resolved
bnovak32
reviewed
Aug 15, 2024
..._raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/workflow_code/Remove_Human_Reads.nf
Outdated
Show resolved
Hide resolved
…low_Documentation/NF_MGRemoveHumanReads-A/workflow_code/README.md to Metagenomics/Remove_human_reads_from_raw_data/Workflow_Documentation/NF_MGRemoveHumanReads-A/README.md corrected readme location and uploaded changes
making some fixes as per Barbara's comments
corrected variable name
small changes for clarity
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
changed WF name, fixed some documentation, and removed the Estimate Host Reads WF from PR @bnovak32 @asaravia-butler