Adding maintainer

nasa · bnovak32 · Jan 15, 2025 · Apr 25, 2024 · Apr 25, 2024 · Apr 25, 2024
commit 1bec5f8ae7202d05acf6b8775b3ed9926f850c28
diff --git a/Microarray/Agilent_1-channel/README.md b/Microarray/Agilent_1-channel/README.md
@@ -23,5 +23,7 @@
 ---
 **Developed by:**  
 Jonathan Oribello  
+
 **Maintained by:**  
-Alexis Torres ([email protected])
+Crystal Han ([email protected])  
+Alexis Torres ([email protected])
diff --git a/Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md b/Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md

 **Parameter Definitions:**

 * `--stdin` - fastq file with the reads contining the cell ID and UMI (reverse reads for samples prepared with the Qiagen UPX kit) 
 * `--bc-pattern` – pattern for the barcode on the read containing the cell ID and UMI; `C`'s indicate placeholders for cell IDs; `N`'s indicate placeholders for UMIs 
 * `--plot-prefix` - instructs the program to output plots to visualize the set of thresholds considered for defining cell barcodes
 * `-L` - specifies whitelist output log file

 **Output Data:**
 - *whitelist.log (whitelist extraction log file)
 - *barcode_counts.png (plot visualizing the knee in the cell barcode count distrubution)
 - *barcode_knee.png (plot visualizing the knee in the cell barcode distrubution)
 - *whitelist.tsv (whitelist output file containing 4 tab-separated columns: 1-whitelist cell IDs, 2-cell IDs that are 1bp different from the respective whitelist cell ID identified, 3-number of whitelisted cell IDs, 4-number of 1bp different cell IDs)
  > **Note1:** Review column 1 of this file for each sample pool and check that all cell IDs for each sample in the respective sample pool are present. If any cell IDs are missing, increase the `--set-cell-number` option by one, and re-run this step. Repeat until all cell IDs for each sample pool are shown in column 1. 
  >

 **Parameter Definitions:**

 * `--stdin` - fastq file with the reads contining the cell ID and UMI (reverse reads for samples prepared with the Qiagen UPX kit) 
 * `--read2-in` - fastq file with the reads contining the sequence of interest (forward reads for samples prepared with the Qiagen UPX kit)
 * `--bc-pattern` – pattern for the barcode on the read containing the cell ID and UMI; `C`'s indicate placeholders for cell IDs; `N`'s indicate placeholders for UMIs 
 * `--stdout` – specifies the path and file name of the output fastq file 
 * `--read2-stdout` - instructs the program to only output the fastq file designated with the `--read2-in` option 
diff --git a/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-A/workflow_code/Snakefile b/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-A/workflow_code/Snakefile
 # snakemake --use-conda --conda-prefix ${CONDA_PREFIX}/envs -j 2 -p

 # `--use-conda` – this specifies to use the conda environments included in the workflow
 # `--conda-prefix` – this allows us to point to where the needed conda environments should be stored. Including this means if we use the workflow on a different dataset somewhere else in the future, it will re-use the same conda environments rather than make new ones. The value listed here, `${CONDA_PREFIX}/envs`, is the default location for conda environments (the variable `${CONDA_PREFIX}` will be expanded to the appropriate location on whichever system it is run on).
 # `-j` – this lets us set how many jobs Snakemake should run concurrently (keep in mind that many of the thread and cpu parameters set in the config.yaml file will be multiplied by this)
 # `-p` – specifies to print out each command being run to the screen

diff --git a/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-A/workflow_code/config.yaml b/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-A/workflow_code/config.yaml
 # snakemake --use-conda --conda-prefix ${CONDA_PREFIX}/envs -j 2 -p

 # `--use-conda` – this specifies to use the conda environments included in the workflow
 # `--conda-prefix` – this allows us to point to where the needed conda environments should be stored. Including this means if we use the workflow on a different dataset somewhere else in the future, it will re-use the same conda environments rather than make new ones. The value listed here, `${CONDA_PREFIX}/envs`, is the default location for conda environments (the variable `${CONDA_PREFIX}` will be expanded to the appropriate location on whichever system it is run on).
 # `-j` – this lets us set how many jobs Snakemake should run concurrently (keep in mind that many of the thread and cpu parameters set in the config.yaml file will be multiplied by this)
 # `-p` – specifies to print out each command being run to the screen

diff --git a/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/README.md b/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/README.md
 # SW_AmpIllumina-B Workflow Information and Usage Instructions <!-- omit in toc -->

 The SW_AmpIllumina-B workflow is curently under development and will be available soon.

 > A beta version of SW_AmpIllumina-B is available under development branch: [dev2-amplicon-add-runsheet-visualizations](https://github.com/nasa/GeneLab_Data_Processing/tree/dev2-amplicon-add-runsheet-visualizations/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B)

diff --git a/.../SW_AmpIllumina-B/examples/runsheet/paired_end_runsheet/GLDS-487_amplicon_v0_runsheet.csv b/.../SW_AmpIllumina-B/examples/runsheet/paired_end_runsheet/GLDS-487_amplicon_v0_runsheet.csv
 lane1TineB1,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB1_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB1_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,Diabetic foot ulcers,lane1TineB1,Not Applicable & Diabetic foot ulcers
 lane1TineB2,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB2_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB2_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,Diabetic foot ulcers,lane1TineB2,Not Applicable & Diabetic foot ulcers
 lane1TineB3,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB3_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB3_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,Diabetic foot ulcers,lane1TineB3,Not Applicable & Diabetic foot ulcers
 lane1TineB4,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB4_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB4_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB4,Not Applicable & contralateral heathy foot
 lane1TineB5,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB5_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB5_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB5,Not Applicable & contralateral heathy foot
 lane1TineB6,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB6_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB6_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB6,Not Applicable & contralateral heathy foot
 lane1TineB7,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB7_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB7_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB7,Not Applicable & contralateral heathy foot

	Parameter Definitions:

	* `--stdin` - fastq file with the reads contining the cell ID and UMI (reverse reads for samples prepared with the Qiagen UPX kit)
Check failure on line 107 in Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md GitHub Actions / Discover typos with codespell `contining ==> containing, continuing`
	* `--bc-pattern` – pattern for the barcode on the read containing the cell ID and UMI; `C`'s indicate placeholders for cell IDs; `N`'s indicate placeholders for UMIs
	* `--plot-prefix` - instructs the program to output plots to visualize the set of thresholds considered for defining cell barcodes
	* `-L` - specifies whitelist output log file

	Output Data:
	- *whitelist.log (whitelist extraction log file)
	- *barcode_counts.png (plot visualizing the knee in the cell barcode count distrubution)
Check failure on line 120 in Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md GitHub Actions / Discover typos with codespell `distrubution ==> distribution`
	- *barcode_knee.png (plot visualizing the knee in the cell barcode distrubution)
Check failure on line 121 in Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md GitHub Actions / Discover typos with codespell `distrubution ==> distribution`
	- *whitelist.tsv (whitelist output file containing 4 tab-separated columns: 1-whitelist cell IDs, 2-cell IDs that are 1bp different from the respective whitelist cell ID identified, 3-number of whitelisted cell IDs, 4-number of 1bp different cell IDs)
	> Note1: Review column 1 of this file for each sample pool and check that all cell IDs for each sample in the respective sample pool are present. If any cell IDs are missing, increase the `--set-cell-number` option by one, and re-run this step. Repeat until all cell IDs for each sample pool are shown in column 1.
	>

	Parameter Definitions:

	* `--stdin` - fastq file with the reads contining the cell ID and UMI (reverse reads for samples prepared with the Qiagen UPX kit)
Check failure on line 147 in Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md GitHub Actions / Discover typos with codespell `contining ==> containing, continuing`
	* `--read2-in` - fastq file with the reads contining the sequence of interest (forward reads for samples prepared with the Qiagen UPX kit)
Check failure on line 148 in Raw_Data_Generation/UPX_kit_for_bulk_RNAseq/Pipeline_GL-DPPD-7108_Versions/GL-DPPD-7108.md GitHub Actions / Discover typos with codespell `contining ==> containing, continuing`
	* `--bc-pattern` – pattern for the barcode on the read containing the cell ID and UMI; `C`'s indicate placeholders for cell IDs; `N`'s indicate placeholders for UMIs
	* `--stdout` – specifies the path and file name of the output fastq file
	* `--read2-stdout` - instructs the program to only output the fastq file designated with the `--read2-in` option
	# snakemake --use-conda --conda-prefix ${CONDA_PREFIX}/envs -j 2 -p

	# `--use-conda` – this specifies to use the conda environments included in the workflow
	# `--conda-prefix` – this allows us to point to where the needed conda environments should be stored. Including this means if we use the workflow on a different dataset somewhere else in the future, it will re-use the same conda environments rather than make new ones. The value listed here, `${CONDA_PREFIX}/envs`, is the default location for conda environments (the variable `${CONDA_PREFIX}` will be expanded to the appropriate location on whichever system it is run on).
Check failure on line 26 in Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-A/workflow_code/Snakefile GitHub Actions / Discover typos with codespell `re-use ==> reuse`
	# `-j` – this lets us set how many jobs Snakemake should run concurrently (keep in mind that many of the thread and cpu parameters set in the config.yaml file will be multiplied by this)
	# `-p` – specifies to print out each command being run to the screen
	# SW_AmpIllumina-B Workflow Information and Usage Instructions <!-- omit in toc -->

	The SW_AmpIllumina-B workflow is curently under development and will be available soon.
Check failure on line 3 in Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/README.md GitHub Actions / Discover typos with codespell `curently ==> currently`

	> A beta version of SW_AmpIllumina-B is available under development branch: [dev2-amplicon-add-runsheet-visualizations](https://github.com/nasa/GeneLab_Data_Processing/tree/dev2-amplicon-add-runsheet-visualizations/Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B)
	lane1TineB1,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB1_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB1_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,Diabetic foot ulcers,lane1TineB1,Not Applicable & Diabetic foot ulcers
	lane1TineB2,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB2_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB2_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,Diabetic foot ulcers,lane1TineB2,Not Applicable & Diabetic foot ulcers
	lane1TineB3,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB3_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB3_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,Diabetic foot ulcers,lane1TineB3,Not Applicable & Diabetic foot ulcers
	lane1TineB4,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB4_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB4_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB4,Not Applicable & contralateral heathy foot
Check failure on line 17 in Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/examples/runsheet/paired_end_runsheet/GLDS-487_amplicon_v0_runsheet.csv GitHub Actions / Discover typos with codespell `heathy ==> healthy` Check failure on line 17 in Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/examples/runsheet/paired_end_runsheet/GLDS-487_amplicon_v0_runsheet.csv GitHub Actions / Discover typos with codespell `heathy ==> healthy`
	lane1TineB5,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB5_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB5_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB5,Not Applicable & contralateral heathy foot
	lane1TineB6,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB6_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB6_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB6,Not Applicable & contralateral heathy foot
	lane1TineB7,16S,Microbiota,Homo sapiens,True,GTGCCAGCMGCCGCGGTAA,GGACTACHVGGGTWTCTAAT,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB7_R1_raw.fastq.gz,https://genelab-data.ndc.nasa.gov/geode-py/ws/studies/OSD-487/download?source=datamanager&file=GLDS-487_Amplicon_lane1TineB7_R2_raw.fastq.gz,_R1_raw.fastq.gz,_R2_raw.fastq.gz,Not Applicable,contralateral heathy foot,lane1TineB7,Not Applicable & contralateral heathy foot