Update Readme

Document where to find pipelines to produce input files.

.gitignore

@@ -1,3 +1,6 @@
 data/*
 tmp/*
 envs/*
+logs/*
+.snakemake
+falcon-comb*

README.md

@@ -1,36 +1,35 @@
-Template workflow folder for Snakemake pipeline
-===============================================
+Pogigwasc gene prediction of Loxodes magnus genome
+===================================================
 
-After cloning this repository, you should change the name of the folder as
-appropriate, and update the remote URL of the repository to a new one for your
-project.
+Snakemake pipeline for gene prediction for Loxodes magnus, which has a genetic
+code with context-dependent stop codons. Introns are first empirically
+predicted with [Intronarrator](https://github.com/Swart-lab/Intronarrator) and
+artifically removed to produce an "intronless" assembly, to run
+[Pogigwasc](https://github.com/Swart-lab/pogigwasc) in `--no-intron` mode. This
+is because the short lengths and unusual length distribution of introns in
+Loxodes are difficult to model with the GHMM in Pogigwasc.
 
+Data
+----
 
-Suggested setup
----------------
+Pipeline and scripts to generate the genome assembly are available from
+[loxodes-assembly-workflow](https://github.com/Swart-lab/loxodes-assembly-workflow)
+repository. Pipeline for the "intronless" assembly is available from
+[loxodes-intronarrator-workflow](https://github.com/Swart-lab/loxodes-intronarrator-workflow).
 
-```bash
-git clone git@github.com:Swart-lab/snakemake-template.git
-mv snakemake-template my-project # rename project folder
-cd my-project
-mkdir data # folder to put project data, gitignored
-mkdir envs # folder for Conda envs produced by workflow, gitignored
-mkdir tmp  # folder for temp files, gitignored
-mkdir nb   # folder for computational notebooks etc.
-git remote remove origin # remove template repo as a remote
-```
+This current pipeline was used for annotation of the MAC and MIC genomes; path
+to reference assembly and names of output files were modified accordingly.
 
-Edit the files `run_snakemake.sh` and/or `run_snakemake_sge.sh` to include
-absolute paths to the working folder and to a Conda environment with Snakemake,
-and modify other settings (e.g. max number of CPUs) as required.
+Paths to input files in the `workflow/config.yaml` file are local paths used in
+the original data analysis. When re-running the pipeline, replace these with
+the actual paths on your system.
 
-Snakemake rules and config files are in the `workflow/` subfolder.
+Curated output from this annotation are included in the [archive of genome
+annotations](https://doi.org/10.17617/3.9QTROS).
 
 
 Running workflow
 ----------------
 
 To run on a local server, use `./run_snakemake.sh` script, and add rule names
 and additional parameters, e.g. `./run_snakemake.sh --dryrun`.
-
-[Documentation for `run_snakemake_sge.sh` TK]

run_snakemake.sh

@@ -11,14 +11,14 @@ set -e
 #  * Conda environments will be created in a subfolder `envs/`
 
 # PATHS
-SNAKEMAKE_ENV=
-WD=
+SNAKEMAKE_ENV=/ebio/ag-swart/home/kbseah/anaconda3/envs/snakemake
+WD=/ebio/abt2_projects/ag-swart-loxodes/annotation/falcon-comb_LmagMIC/pogigwasc_intronless
 
 # activate snakemake conda environment
 source activate $SNAKEMAKE_ENV
 
 snakemake \
---cores 24 \
+--cores 16 \
 --configfile $WD/workflow/config.yaml \
 --use-conda \
 --conda-frontend mamba \

workflow/config.yaml

@@ -1,9 +1,9 @@
 falcon-comb_LmagMIC:
-  ref_orig:
+  ref_orig: # Original reference genome assembly
     /ebio/abt2_projects/ag-swart-loxodes/assembly/falcon-comb_LmagMIC/scaffolds.fasta
-  ref_intronless_masked:
+  ref_intronless_masked: # Intronless assembly produced by Intronarrator
     /ebio/abt2_projects/ag-swart-loxodes/annotation/falcon-comb_LmagMIC/intronarrator/falcon-comb_LmagMIC.0.2.minus_introns.ncRNA_hard_masked.fa
-  realtrons_gff:
+  realtrons_gff: # Intron annotation GFF3 file produced by intronarrator
     /ebio/abt2_projects/ag-swart-loxodes/annotation/falcon-comb_LmagMIC/intronarrator/all.realtrons.0.2.noalt.gff
-  trf_min1000:
+  trf_min1000: # Low-complexity sequence annotation GFF3
     /ebio/abt2_projects/ag-swart-loxodes/annotation/falcon-comb_LmagMIC/trf/falcon-comb_LmagMIC.trf.no_overlap.min1000.merge.bed