[DEV_Metagenomics_Illumina] Minor documentation updates (#151)

- Pipeline doc
  - fixed typo in sed command
- NF workflow doc
  - added explicit definitions for all profiles available
  - removed slurm from example command-line calls
  - updated headings to adjust slurm removal
- simplified instructions for different run approaches
- added conda env configuration information as additional information under the conda profile definition.

Author: bnovak32

Metagenomics/Illumina/Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md

@@ -543,7 +543,7 @@ awk -F $'\t' ' BEGIN { OFS=FS } { if ( $3 == "lineage" ) { print $1,$3,$5,$6,$7,
     else if ( $2 == "ORF has no hit to database" || $2 ~ /^no taxid found/ ) \
     { print $1,"NA","NA","NA","NA","NA","NA","NA","NA" } else { n=split($3,lineage,";"); \
     print $1,lineage[n],$5,$6,$7,$8,$9,$10,$11 } } ' sample-1-gene-tax-out.tmp | \
-    sed no support/NA/g' | sed 's/superkingdom/domain/' | sed 's/# ORF/gene_ID/' | \
+    sed 's/no support/NA/g' | sed 's/superkingdom/domain/' | sed 's/# ORF/gene_ID/' | \
     sed 's/lineage/taxid/'  > sample-1-gene-tax-out.tsv
 ```
 

Metagenomics/Illumina/Workflow_Documentation/NF_MGIllumina/README.md

@@ -4,7 +4,7 @@
 
 ### Implementation Tools
 
-The current GeneLab Illumina metagenomics sequencing data processing pipeline (MGIllumina-A), [GL-DPPD-7107-A.md](../../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md), is implemented as a [Nextflow](https://nextflow.io/) DSL2 workflow and utilizes [Singularity](https://docs.sylabs.io/guides/3.10/user-guide/introduction.html) containers, [docker](https://docs.docker.com/get-started/) containers, or [conda](https://docs.conda.io/en/latest/) environments to install/run all tools. This workflow is run using the command line interface (CLI) of any unix-based system.  While knowledge of creating workflows in Nextflow is not required to run the workflow as is, [the Nextflow documentation](https://nextflow.io/docs/latest/index.html) is a useful resource for users who want to modify and/or extend this workflow. 
+The current GeneLab Illumina metagenomics sequencing data processing pipeline (MGIllumina-A), [GL-DPPD-7107-A.md](../../Pipeline_GL-DPPD-7107_Versions/GL-DPPD-7107-A.md), is implemented as a [Nextflow](https://nextflow.io/) DSL2 workflow and utilizes [Singularity](https://docs.sylabs.io/guides/3.10/user-guide/introduction.html) containers, [Docker](https://docs.docker.com/get-started/) containers, or [conda](https://docs.conda.io/en/latest/) environments to install/run all tools. This workflow is run using the command line interface (CLI) of any unix-based system.  While knowledge of creating workflows in Nextflow is not required to run the workflow as is, [the Nextflow documentation](https://nextflow.io/docs/latest/index.html) is a useful resource for users who want to modify and/or extend this workflow. 
 
 > **Note on reference databases**  
 > Many reference databases are relied upon throughout this workflow. They will be installed and setup automatically the first time the workflow is run. All together, after installed and unpacked, they will take up about about 340 GB of storage, but they may also require up to 500GB during installation and initial un-packing, so be sure there is enough room on your system before running the workflow.
@@ -13,24 +13,18 @@ The current GeneLab Illumina metagenomics sequencing data processing pipeline (M
 
 ## Utilizing the Workflow
 
-1. [Installing Nextflow, Singularity, and conda](#1-install-nextflow-and-singularity)  
+1. [Installing Nextflow, Singularity, and conda](#1-installing-nextflow-singularity-and-conda)  
    1a. [Install Nextflow and conda](#1a-install-nextflow-and-conda)  
    1b. [Install Singularity](#1b-install-singularity)  
-
 2. [Download the workflow files](#2-download-the-workflow-files)  
-
 3. [Fetch Singularity Images](#3-fetch-singularity-images)  
-
 4. [Run the workflow](#4-run-the-workflow)  
-   4a. [Approach 1: Run slurm jobs in Singularity containers with OSD or GLDS accession as input](#4a-approach-1-run-slurm-jobs-in-singularity-containers-with-osd-or-glds-accession-as-input)  
-   4b. [Approach 2: Run slurm jobs in Singularity containers with a csv file as input](#4b-approach-2-run-slurm-jobs-in-singularity-containers-with-a-csv-file-as-input)  
-   4c. [Approach 3: Run jobs locally in conda environments and specify the path to one or more existing conda environments](#4c-approach-3-run-jobs-locally-in-conda-environments-and-specify-the-path-to-one-or-more-existing-conda-environments)  
-   4d. [Modify parameters and cpu resources in the Nextflow config file](#4d-modify-parameters-and-cpu-resources-in-the-nextflow-config-file)  
-
+   4a. [Approach 1: Start with OSD or GLDS accession as input](#4a-approach-1-start-with-an-osd-or-glds-accession-as-input)    
+   4b. [Approach 2: Start with a runsheet csv file as input](#4b-approach-2-start-with-a-runsheet-csv-file-as-input)  
+   4c. [Modify parameters and compute resources in the Nextflow config file](#4c-modify-parameters-and-compute-resources-in-the-nextflow-config-file)
 5. [Workflow outputs](#5-workflow-outputs)  
    5a. [Main outputs](#5a-main-outputs)  
    5b. [Resource logs](#5b-resource-logs)  
-
 6. [Post Processing](#6-post-processing)  
 
 <br>
@@ -125,26 +119,18 @@ Take care to use the proper number of hyphens for each argument.
 
 <br>
 
-#### 4a. Approach 1: Run slurm jobs in Singularity containers with OSD or GLDS accession as input
+#### 4a. Approach 1: Start with an OSD or GLDS accession as input
 
 ```bash
-nextflow run main.nf -resume -profile slurm,singularity --accession OSD-574
+nextflow run main.nf -resume -profile singularity --accession OSD-574
 ```
 
 <br>
 
-#### 4b. Approach 2: Run slurm jobs in Singularity containers with a csv file as input
+#### 4b. Approach 2: Start with a runsheet csv file as input
 
 ```bash
-nextflow run main.nf -resume -profile slurm,singularity  --input_file PE_file.csv
-```
-
-<br>
-
-#### 4c. Approach 3: Run jobs locally in conda environments and specify the path to one or more existing conda environment(s)
-
-```bash
-nextflow run main.nf -resume -profile mamba --input_file SE_file.csv --conda_megahit <path/to/existing/conda/environment>
+nextflow run main.nf -resume -profile singularity  --input_file PE_file.csv
 ```
 
 <br>
@@ -155,24 +141,34 @@ nextflow run main.nf -resume -profile mamba --input_file SE_file.csv --conda_meg
 
 * `-resume` - Resumes workflow execution using previously cached results
 
-* `-profile` – Specifies the configuration profile(s) to load; `singularity` instructs Nextflow to setup and use Singularity for all software called in the workflow. 
-   > Note: Use `docker` to instruct Nextflow to use the Docker container environment instead.
+* `-profile` – Specifies the configuration profile(s) to load (multiple options can be provided as a comma-separated list)
+   * Software environment profile options (choose one):
+      * `singularity` - instructs Nextflow to use Singularity container environments
+      * `docker` - instructs Nextflow to use Docker container environments
+      * `conda` - instructs Nextflow to use conda environments via the conda package manager. By default, Nextflow will create environments at runtime using the yaml files in the [workflow_code/envs](workflow_code/envs/) folder. You can change this behavior by using the `--conda_*` workflow parameters or by editing the [nextflow.config](workflow_code/nextflow.config) file to specify a centralized conda environments directory via the `conda.cacheDir` parameter
+      * `mamba` - instructs Nextflow to use conda environments via the mamba package manager. 
+   * Other option (can be combined with the software environment option above):
+      * `slurm` - instructs Nextflow to use the [Slurm cluster management and job scheduling system](https://slurm.schedmd.com/overview.html) to schedule and run the jobs on a Slurm HPC cluster.
 
 * `--accession` – A Genelab / OSD accession number e.g. OSD-574.
-   > *Required only if you would like to pull and process data directly from OSDR*
+   > *Required only if you would like to download and process data directly from OSDR*
+
+* `--input_file` –  A single-end or paired-end runsheet csv file containing assay metadata for each sample, including sample_id, forward, reverse, and/or paired. Please see the [runsheet documentation](./examples/runsheet) in this repository for examples on how to format this file.
+   > *Required only if `--accession` is not passed as an argument*
+
+<br> 
 
-* `--input_file` –  A single-end or paired-end input csv file containing assay metadata for each sample, including sample_id, forward, reverse, and/or paired. Please see the [runsheet documentation](./examples/runsheet) in this repository for examples on how to format this file.
-   > *Required only if --accession is not passed as an argument*
+> See `nextflow run -h` and [Nextflow's CLI run command documentation](https://nextflow.io/docs/latest/cli.html#run) for more options and details on how to run Nextflow.  
+> For additional information on editing the `nextflow.config` file, see [Step 4d](#4d-modify-parameters-and-cpu-resources-in-the-nextflow-config-file) below.   
 
-> See `nextflow run -h` and [Nextflow's CLI run command documentation](https://nextflow.io/docs/latest/cli.html#run) for more options and details on how to run Nextflow.
 
 <br>
 
-#### 4d. Modify parameters and cpu resources in the nextflow config file
+#### 4c. Modify parameters and compute resources in the Nextflow config file
 
-Additionally, the parameters and workflow resources can be directly specified in the nextflow.config file. For detailed instructions on how to modify and set parameters in the nextflow.config file, please see the [documentation here](https://www.nextflow.io/docs/latest/config.html).
+Additionally, all parameters and workflow resources can be directly specified in the [nextflow.config](./workflow_code/nextflow.config) file. For detailed instructions on how to modify and set parameters in the config file, please see the [documentation here](https://www.nextflow.io/docs/latest/config.html).
 
-Once you've downloaded the workflow template, you can modify the parameters in the `params` scope and cpus/memory requirements in the `process` scope in your downloaded version of the [nextflow.config](workflow_code/nextflow.config) file as needed in order to match your dataset and system setup. Additionally, if necessary, you'll need to modify each variable in the [nextflow.config](workflow_code/nextflow.config) file to be consistent with the study you want to process and the machine you're using.
+Once you've downloaded the workflow template, you can modify the parameters in the `params` scope and cpus/memory requirements in the `process` scope in your downloaded version of the [nextflow.config](workflow_code/nextflow.config) file as needed in order to match your dataset and system setup. Additionally, if necessary, you can modify each variable in the [nextflow.config](workflow_code/nextflow.config) file to be consistent with the study you want to process and the computer you're using for processing.
 
 <br>
 
@@ -214,7 +210,7 @@ nextflow run post_processing.nf --help
 To generate the post-processing files after running the main processing workflow successfully, modify and set the parameters in [post_processing.config](workflow_code/post_processing.config), then run the following command:
 
 ```bash
-nextflow -C post_processing.config run post_processing.nf -resume -profile slurm,singularity
+nextflow -C post_processing.config run post_processing.nf -resume -profile singularity
 ``` 
 
 The outputs of the post-processing workflow are described below: