Complete renaming of project

adamd3 · Nov 16, 2024 · 074c9b5 · 074c9b5
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diff --git a/README.md b/README.md
@@ -1,8 +1,7 @@
-![StrainQuant](docs/images/StrainQuant_light.png#gh-light-mode-only) ![StrainQuant](docs/images/StrainQuant_dark.png#gh-dark-mode-only)
+# StrainQuant
 
 ![StrainQuant](https://github.com/adamd3/StrainQuant/actions/workflows/ci.yml/badge.svg)
 
-
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
@@ -41,22 +40,23 @@ You can run with [`Docker`](https://www.docker.com/) or [`Singularity`](https://
 The `-resume` parameter will re-start the pipeline if it has been previously run.
 
 Explanation of parameters:
+
 - `meta_file`: metadata file (see below).
 - `gpa_file`: gene presence/absence file from Panaroo (see below).
 - `perc`: defines the minimum percent of strains containing a gene for inclusion in the analysis (for example, --perc 99 means that a gene must be present in 99% of strains for it to be included).
 - `strandedness`: Strandedness of the reads. 0 = unstranded, 1 = forward-stranded, 2 = reverse-stranded. Default = 2.
-- `fragment_len`:  Estimated average fragment length for kallisto transcript quantification (only required for single-end reads). Default = 150.
+- `fragment_len`: Estimated average fragment length for kallisto transcript quantification (only required for single-end reads). Default = 150.
 - `fragment_sd`: Estimated standard deviation of fragment length for kallisto transcript quantification (only required for single-end reads). Default = 20.
 - `norm_method`: how to perform size-factor scaling of counts (default method = `DESeq2`). Other options: `TMM` (edgeR).
 - `group`: group for plots - must be one of the columns in metadata file.
 - `skip_trimming`: do not trim adaptors from reads.
 - `outdir`: the output directory where the results will be saved (Default: `./results`).
 
-
 ## Required input
 
-- __Metadata file__: tab-delimited (TSV) file, which must contain at least the following named columns:
-  - `rna_sample_id`: name of the RNA-Seq data file 
+- **Metadata file**: tab-delimited (TSV) file, which must contain at least the following named columns:
+
+  - `rna_sample_id`: name of the RNA-Seq data file
   - `dna_sample_id`: gene sequence sample identifier (must match the column name in the Panaroo gene presence/absence file)
   - `sample_name`: unique identifier for the sample
   - `fastq1`: path to fastq file for RNA-Seq data
@@ -66,35 +66,35 @@ Explanation of parameters:
 
   Example:
 
-    ```console
-    rna_sample_id	dna_sample_id	sample_name	majority_ST	level7000	acsA	aroE	guaA	mutL	nuoD	ppsA	trpE	patient	collection_date	cohort	infection_type	fastq1	fastq2	fasta	
-    SRX5123742	SRR8737281	ZG301975	313	2	47	8	7	6	8	11	40	ZG301975		hzi_amr		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123742_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737281.fna	
-    SRX5123741	SRR8737282	ZG205864	111	3	17	5	5	4	4	4	3	ZG205864		hzi_amr		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123741_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737282.fna	
-    SRX5123744	SRR8737283	ZG302367	274	4	23	5	11	7	1	12	7	ZG302367		hzi_amr	ear infection	https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123744_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737283.fna	
-    ```
+  ```console
+  rna_sample_id	dna_sample_id	sample_name	majority_ST	level7000	acsA	aroE	guaA	mutL	nuoD	ppsA	trpE	patient	collection_date	cohort	infection_type	fastq1	fastq2	fasta
+  SRX5123742	SRR8737281	ZG301975	313	2	47	8	7	6	8	11	40	ZG301975		hzi_amr		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123742_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737281.fna
+  SRX5123741	SRR8737282	ZG205864	111	3	17	5	5	4	4	4	3	ZG205864		hzi_amr		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123741_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737282.fna
+  SRX5123744	SRR8737283	ZG302367	274	4	23	5	11	7	1	12	7	ZG302367		hzi_amr	ear infection	https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123744_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737283.fna
+  ```
 
-- __Gene presence-absence file__: CSV-format output produced by [`Panaroo`](https://gtonkinhill.github.io/panaroo/).
+- **Gene presence-absence file**: CSV-format output produced by [`Panaroo`](https://gtonkinhill.github.io/panaroo/).
   See below example (truncated):
 
-    ```console
-    Gene,Non-unique Gene name,Annotation,Pseudomonas_aeruginosa_PAO1_107_converted,SRR8737281,SRR8737282
-    group_25769,,Protein of unknown function (DUF2845),PGD112333,SRR8737281_00662,SRR8737282_00657
-    group_25760,;hypothetical protein,hypothetical protein;topoisomerase IIProtein of unknown function (DUF2790);Protein of unknown function (DUF2790);acyl- n-acyltransferaseUncharacterized protein conserved in bacteriaProtein of unknown function DUF482;,PGD109272,SRR8737281_05540,SRR8737282_06520
-    group_25759,;hypothetical protein,Protein of unknown function (DUF3309);,PGD109276,SRR8737281_05538,SRR8737282_03481
-    rubA2~~~Rubredoxin2,rubA2;Rubredoxin 2,rubredoxinRubredoxin-2anaerobic nitric oxide reductase flavorubredoxinRubredoxinRubredoxin;,PGD113575,SRR8737281_00021,SRR8737282_05845
-    bfr_2~~~bacterioferritin,bfr_2;bacterioferritin,bacterioferritinBacterioferritinbacterioferritinBacterioferritin (cytochrome b1)bacterioferritinFerritin-like domain;,PGD109882,SRR8737281_05955,SRR8737282_01475
-    mtnB~~~probablesugaraldolase,mtnB;probable sugar aldolase,methylthioribulose-1-phosphate dehydrataseMethylthioribulose-1-phosphate dehydratasemethylthioribulose-1-phosphate dehydrataseRibulose-5-phosphate 4-epimerase and related epimerases and aldolasesmethylthioribulose-1-phosphate dehydrataseClass II Aldolase and Adducin N-terminal domain;,PGD106137,SRR8737281_02504,SRR8737282_00940
-    epd_2~~~epd_1~~~epd,epd_2;epd_1;epd,D-erythrose-4-phosphate dehydrogenaseD-erythrose-4-phosphate dehydrogenaseerythrose 4-phosphate dehydrogenaseerythrose-4-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase C-terminal domain;D-erythrose-4-phosphate dehydrogenaseD-erythrose-4-phosphate dehydrogenaseerythrose 4-phosphate dehydrogenaseTransketolaseerythrose-4-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase C-terminal domain,PGD103840,SRR8737281_03107,SRR8737282_02473
-    emrE,emrE,SMR multidrug efflux transporterMethyl viologen resistance protein Cmultidrug efflux proteinMembrane transporters of cations and cationic drugsphosphonate utilization associated putative membrane proteinSmall Multidrug Resistance protein;SMR multidrug efflux transporterMethyl viologen resistance protein Cmultidrug efflux proteinMembrane transporters of cations and cationic drugsSmall Multidrug Resistance protein,PGD112851,SRR8737281_00400,SRR8737282_00337
-    purA_1~~~purA_2~~~purA,purA_1;purA_2;purA,adenylosuccinate synthetaseAdenylosuccinate synthetaseadenylosuccinate synthetaseadenylosuccinate synthaseAdenylosuccinate synthetase,PGD112747,SRR8737281_00453,SRR8737282_00390
-    ```
+  ```console
+  Gene,Non-unique Gene name,Annotation,Pseudomonas_aeruginosa_PAO1_107_converted,SRR8737281,SRR8737282
+  group_25769,,Protein of unknown function (DUF2845),PGD112333,SRR8737281_00662,SRR8737282_00657
+  group_25760,;hypothetical protein,hypothetical protein;topoisomerase IIProtein of unknown function (DUF2790);Protein of unknown function (DUF2790);acyl- n-acyltransferaseUncharacterized protein conserved in bacteriaProtein of unknown function DUF482;,PGD109272,SRR8737281_05540,SRR8737282_06520
+  group_25759,;hypothetical protein,Protein of unknown function (DUF3309);,PGD109276,SRR8737281_05538,SRR8737282_03481
+  rubA2~~~Rubredoxin2,rubA2;Rubredoxin 2,rubredoxinRubredoxin-2anaerobic nitric oxide reductase flavorubredoxinRubredoxinRubredoxin;,PGD113575,SRR8737281_00021,SRR8737282_05845
+  bfr_2~~~bacterioferritin,bfr_2;bacterioferritin,bacterioferritinBacterioferritinbacterioferritinBacterioferritin (cytochrome b1)bacterioferritinFerritin-like domain;,PGD109882,SRR8737281_05955,SRR8737282_01475
+  mtnB~~~probablesugaraldolase,mtnB;probable sugar aldolase,methylthioribulose-1-phosphate dehydrataseMethylthioribulose-1-phosphate dehydratasemethylthioribulose-1-phosphate dehydrataseRibulose-5-phosphate 4-epimerase and related epimerases and aldolasesmethylthioribulose-1-phosphate dehydrataseClass II Aldolase and Adducin N-terminal domain;,PGD106137,SRR8737281_02504,SRR8737282_00940
+  epd_2~~~epd_1~~~epd,epd_2;epd_1;epd,D-erythrose-4-phosphate dehydrogenaseD-erythrose-4-phosphate dehydrogenaseerythrose 4-phosphate dehydrogenaseerythrose-4-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase C-terminal domain;D-erythrose-4-phosphate dehydrogenaseD-erythrose-4-phosphate dehydrogenaseerythrose 4-phosphate dehydrogenaseTransketolaseerythrose-4-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase C-terminal domain,PGD103840,SRR8737281_03107,SRR8737282_02473
+  emrE,emrE,SMR multidrug efflux transporterMethyl viologen resistance protein Cmultidrug efflux proteinMembrane transporters of cations and cationic drugsphosphonate utilization associated putative membrane proteinSmall Multidrug Resistance protein;SMR multidrug efflux transporterMethyl viologen resistance protein Cmultidrug efflux proteinMembrane transporters of cations and cationic drugsSmall Multidrug Resistance protein,PGD112851,SRR8737281_00400,SRR8737282_00337
+  purA_1~~~purA_2~~~purA,purA_1;purA_2;purA,adenylosuccinate synthetaseAdenylosuccinate synthetaseadenylosuccinate synthetaseadenylosuccinate synthaseAdenylosuccinate synthetase,PGD112747,SRR8737281_00453,SRR8737282_00390
+  ```
 
 ## Output
 
-1. __trim_galore__ directory containing adaptor-trimmed RNA-Seq files and FastQC results.
-2. __gene_counts__ directory containing:
-    1. `gene_set_ST.tsv`: the subset of genes included in analysis.
-    2. `raw_counts.tsv`: merged read counts per gene, scaled to the median gene length across strains.
-    3. `norm_counts.tsv`: size factor scaled counts (normalised for library size).
-    4. `rpkm_counts.tsv`: size factor scaled and gene length-scaled counts, expressed as reads per kilobase per million mapped reads (RPKM) (normalised for library size and gene length).
-3. __umap_samples__ directory containing UMAP visualisation of gene expression across strains.
+1. **trim_galore** directory containing adaptor-trimmed RNA-Seq files and FastQC results.
+2. **gene_counts** directory containing:
+   1. `gene_set_ST.tsv`: the subset of genes included in analysis.
+   2. `raw_counts.tsv`: merged read counts per gene, scaled to the median gene length across strains.
+   3. `norm_counts.tsv`: size factor scaled counts (normalised for library size).
+   4. `rpkm_counts.tsv`: size factor scaled and gene length-scaled counts, expressed as reads per kilobase per million mapped reads (RPKM) (normalised for library size and gene length).
+3. **umap_samples** directory containing UMAP visualisation of gene expression across strains.
diff --git a/docs/images/OrthoQuant_pipeline.png b/docs/images/OrthoQuant_pipeline.png
diff --git a/test_data/meta_merged.txt b/test_data/meta_merged.txt
@@ -1,5 +1,5 @@
 rna_sample_id	dna_sample_id	sample_name	majority_ST	level7000	acsA	aroE	guaA	mutL	nuoD	ppsA	trpE	patient	collection_date	cohort	infection_type	fastq1	fastq2	fasta	
-SRX5123742	SRR8737281	ZG301975	313	2	47	8	7	6	8	11	40	ZG301975		hzi_amr		https://raw.githubusercontent.com/adamd3/OrthoQuant/main/test_data/SRX5123742_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/OrthoQuant/main/test_data/SRR8737281.fna	
-SRX5123741	SRR8737282	ZG205864	111	3	17	5	5	4	4	4	3	ZG205864		hzi_amr		https://raw.githubusercontent.com/adamd3/OrthoQuant/main/test_data/SRX5123741_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/OrthoQuant/main/test_data/SRR8737282.fna	
-SRX5123744	SRR8737283	ZG302367	274	4	23	5	11	7	1	12	7	ZG302367		hzi_amr	ear infection	https://raw.githubusercontent.com/adamd3/OrthoQuant/main/test_data/SRX5123744_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/OrthoQuant/main/test_data/SRR8737283.fna	
+SRX5123742	SRR8737281	ZG301975	313	2	47	8	7	6	8	11	40	ZG301975		hzi_amr		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123742_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737281.fna	
+SRX5123741	SRR8737282	ZG205864	111	3	17	5	5	4	4	4	3	ZG205864		hzi_amr		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123741_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737282.fna	
+SRX5123744	SRR8737283	ZG302367	274	4	23	5	11	7	1	12	7	ZG302367		hzi_amr	ear infection	https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRX5123744_T1_sub.fq.gz		https://raw.githubusercontent.com/adamd3/StrainQuant/main/test_data/SRR8737283.fna