Update README

MPI-EVA-Archaeogenetics · Nov 4, 2024 · ead76a5 · ead76a5
1 parent 76a2e11
commit ead76a5
Showing 1 changed file with 72 additions and 46 deletions.
diff --git a/README.md b/README.md
@@ -4,25 +4,27 @@ Automated nf-core/eager processing of Autorun output bams.
 
 ## Quickstart
 
-- Run `prepare_eager_tsv.R` for human SG or TF data for a given sequencing batch:
+- Run `prepare_eager_tsv.R` for human SG, TF, RP, or RM data for a given sequencing batch:
 
     ```bash
     prepare_eager_tsv.R -s <batch_Id> -a SG -o eager_inputs/ -d .eva_credentials
     prepare_eager_tsv.R -s <batch_Id> -a TF -o eager_inputs/ -d .eva_credentials
+    prepare_eager_tsv.R -s <batch_Id> -a RP -o eager_inputs/ -d .eva_credentials
+    prepare_eager_tsv.R -s <batch_Id> -a RM -o eager_inputs/ -d .eva_credentials
     ```
 
 - Run eager with the following script, which then runs on the generated TSV files:
 
     ```bash
-    run_Eager.sh
+    run_Eager.sh -a
     ```
 
 ⚠️ For some library preparation protocols and external libraries, UDG treatment cannot be reliably inferred, and errors will be thrown.
 In such cases, an eager input TSV will still be created, but UDG treatment for affected libraries will be set to 'Unknown' and needs to be manually edited.
 
 ## Autorun.config
 
-Contains the `autorun`, `SG` and `TF` profiles.
+Contains the `autorun`, `local_paths`, `SG`, `TF`, `RP`, and `RM`  profiles.
 
 ### autorun
 
@@ -43,43 +45,51 @@ The standardised parameters for processing human shotgun data.
 
 The standardised parameters for processing human 1240k capture data.
 
-## prepare_eager_tsv.R
-
-An R script that when given a sequencing batch ID, Autorun Analysis type and PANDORA credentials will create/update eager input TSV files for further processing.
-
-```bash
-Usage: ./prepare_eager_tsv.R [options] .credentials
+### RP
 
-Options:
-    -h, --help
-        Show this help message and exit
+The standardised parameters for processing human Twist capture data.
 
-    -s SEQUENCING_BATCH_ID, --sequencing_batch_id=SEQUENCING_BATCH_ID
-        The Pandora sequencing batch ID to update eager input for. A TSV file will be prepared
-            for each individual in this run, containing all relevant processed BAM files
-            from the individual
+### RM
 
-    -a ANALYSIS_TYPE, --analysis_type=ANALYSIS_TYPE
-        The analysis type to compile the data from. Should be one of: 'SG', 'TF'.
+The standardised parameters for processing human Twist+MT capture data.
 
-    -r, --rename
-        Changes all dots (.) in the Library_ID field of the output to underscores (_).
-            Some tools used in nf-core/eager will strip everything after the first dot (.)
-            from the name of the input file, which can cause naming conflicts in rare cases.
+## prepare_eager_tsv.R
 
-    -w WHITELIST, --whitelist=WHITELIST
-            An optional file that includes the IDs of whitelisted individuals,
-                    one per line. Only the TSVs for these individuals will be updated.
+An R script that when given a sequencing batch ID, Autorun Analysis type and PANDORA credentials will create/update eager input TSV files for further processing.
 
-    -o OUTDIR/, --outDir=OUTDIR/
-        The desired output directory. Within this directory, one subdirectory will be 
-            created per analysis type, within that one subdirectory per individual ID,
-            and one TSV within each of these directory.
+```bash
+Usage: ./scripts/prepare_eager_tsv.R [options] .credentials
 
-    -d, --debug_output
-        When provided, the entire result table for the run will be saved as '<seq_batch_ID>.results.txt'.
-            Helpful to check all the output data in one place.
 
+Options:
+	-h, --help
+		Show this help message and exit
+
+	-s SEQUENCING_BATCH_ID, --sequencing_batch_id=SEQUENCING_BATCH_ID
+		The Pandora sequencing batch ID to update eager input for. A TSV file will be prepared
+			for each individual in this run, containing all relevant processed BAM files
+			from the individual
+
+	-a ANALYSIS_TYPE, --analysis_type=ANALYSIS_TYPE
+		The analysis type to compile the data from. Should be one of: 'SG', 'TF', 'RP', 'RM'.
+
+	-r, --rename
+		Changes all dots (.) in the Library_ID field of the output to underscores (_).
+			Some tools used in nf-core/eager will strip everything after the first dot (.)
+			from the name of the input file, which can cause naming conflicts in rare cases.
+
+	-w WHITELIST, --whitelist=WHITELIST
+		An optional file that includes the IDs of whitelisted individuals,
+			one per line. Only the TSVs for these individuals will be updated.
+
+	-o OUTDIR, --outDir=OUTDIR
+		The desired output directory. Within this directory, one subdirectory will be 
+			created per analysis type, within that one subdirectory per individual ID,
+			and one TSV within each of these directory.
+
+	-d, --debug_output
+		When provided, the entire result table for the run will be saved as '<seq_batch_ID>.results.txt'.
+			Helpful to check all the output data in one place.
 Note: a valid sidora .credentials file is required. Contact the Pandora/Sidora team for details.
 ```
 
@@ -88,13 +98,21 @@ The eager input TSVs will be created in the following directory structure, given
 ```text
 eager_inputs
 ├── SG
-│   └──IND
-│       ├── IND001
-│       └── IND002
-└── TF
-    └──IND
-         ├── IND001
-         └── IND002
+│   └──ABC
+│       ├── ABC001
+│       └── ABC002
+├── TF
+│   └──ABC
+│       ├── ABC001
+│       └── ABC002
+├── RP
+│   └──ABC
+│       ├── ABC001
+│       └── ABC002
+└── RM
+    └──ABC
+         ├── ABC001
+         └── ABC002
 ```
 
 Alongside each created TSV is a file named `autorun_eager_version.txt`, which states the version of Autorun_eager used.
@@ -112,13 +130,21 @@ The outputs are saved with the same directory structure as the inputs, but in a
 ```text
 eager_outputs
 ├── SG
-│   └──IND
-│       ├── IND001
-│       └── IND002
-└── TF
-    └──IND
-         ├── IND001
-         └── IND002
+│   └──ABC
+│       ├── ABC001
+│       └── ABC002
+├── TF
+│   └──ABC
+│       ├── ABC001
+│       └── ABC002
+├── RP
+│   └──ABC
+│       ├── ABC001
+│       └── ABC002
+└── RM
+    └──ABC
+         ├── ABC001
+         └── ABC002
 ```
 
 This script recognises the `-a/--array` option. When this is provided, instead of running eager jobs in sequence, a temporary file is created named `$(date +'%y%m%d_%H%M')_Autorun_eager_queue.txt` that includes the command line of all eager jobs to-be-ran, one per line. An "Autorun_eager spawner" (`AE_spawner`) array job is then submitted using `qsub`, which uses a secondary script named `scripts/submit_as_array.sh` to submit the command in each line of the temporary file as a separate task. In this manner, 10 eager runs can be ran in parallel. Logs for these jobs will then be added to a directory named `array_Logs/<temp_file_name>/`.