readme update

README.md

@@ -32,78 +32,84 @@ pip3 install gitdb2
 
 You have to set 2 files:
 
-* [01_infos/all_samples.tsv](01_infos/all_samples.tsv)
-* [01_infos/config.yaml](01_infos/config_test.yaml)
+* `RAPIDRUN_METADATA` *e.g.* [all_samples.tsv](resources/test/all_samples.tsv)
+* `CONFIG_FILE` *e.g.* [config/config.yaml]
 
 
 # The Workflow
 
 ## 1. Set rapidrun 
 
-Indicate the path of [01_infos/all_samples.tsv](01_infos/all_samples.tsv) file in the `fichiers` `rapidrun` field in [01_infos/config.yaml](01_infos/config_test.yaml)
+Indicate the absolute path of rapidrun metadata table [all_samples.tsv](resources/test/all_samples.tsv) in the `fichiers` `rapidrun` field in [config/config.yaml](config/)
 
 
 ```
-CONFIGFILE=01_infos/config_test.yaml
-snakemake --configfile $CONFIGFILE -s readwrite_rapidrun_demultiplexing.py
+cd 01_settings
+snakemake --configfile "../"$CONFIGFILE -s readwrite_rapidrun_demultiplexing.py --cores $CORES
+cd ..
 ```
-This command will read [01_infos/all_samples.tsv](01_infos/all_samples.tsv) and return a file [01_infos/all_demultiplex.csv](01_infos/all_demultiplex.csv) which can be used to process rapidrun data in the next steps of the workflow.
+This command will read `CONFIGFILE` and the `RAPIDRUN_METADATA` then return a file [results/01_settings/all_demultiplex.csv](results/01_settings/) which can be used to process rapidrun data in the next steps of the workflow.
 
-[01_infos/all_demultiplex.csv](01_infos/all_demultiplex.csv) has 14 fields : *demultiplex,projet,marker,run,plaque,sample,barcode5,barcode3,primer5,primer3,min_f,min_r,lenBarcode5,lenBarcode3* and each row is an unique sample which belong to an unique marker and a project.
+[results/01_settings/all_demultiplex.csv](results/01_settings/) has 14 fields : *demultiplex,projet,marker,run,plaque,sample,barcode5,barcode3,primer5,primer3,min_f,min_r,lenBarcode5,lenBarcode3* and each row is an unique sample which belong to an unique marker and a project.
 
 ## 2 Assembly
 
 ```
-CORES=16
-CONFIGFILE=01_infos/config_test.yaml
 cd 02_assembly
-snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
+cd ..
 ```
 
-Merge paired-end sequences and remove unaligned sequences records.
+Merge paired-end sequences and remove unaligned sequences records. Results are stored into [results/02_assembly](results/02_assembly)
 
 ## 3 Demultiplexing
 
 ```
-cd 03_demultiplexing
-snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+cd 03_demultiplex
+snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
+cd ..
 ```
 
-The tags correspond to short and specific sequences added on the 5’ end of each primer to distinguish the different samples
+The tags correspond to short and specific sequences added on the 5’ end of each primer to distinguish the different samples.
+Check results of demultiplexing into [results/03_demultiplex](results/03_demultiplex)
 
 ## 4 Filter samples
 
 ```
 cd 04_filter_samples
-snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
+cd ..
 ```
 
 For each sample, dereplicate sequences, remove sequences with a given length, remove sequences with IUAPC ambiguity, remove PCR clone, remove sequences which are classified as 'internal' by `obiclean`
 
+Check results into [results/04_filter_samples](results/04_filter_samples)
+
 ## 5 Concatenate samples into runs
 
 ```
-for projet in `ls 04_filter_samples/04_filtered/`;
+for projet in `ls results/04_filter_samples/04_filtered/`;
 do 
- for marker in `ls 04_filter_samples/04_filtered/${projet}/`;
+ for marker in `ls results/04_filter_samples/04_filtered/${projet}/`;
  do
-  for run in `ls 04_filter_samples/04_filtered/${projet}/${marker}/`;
+  for run in `ls results/04_filter_samples/04_filtered/${projet}/${marker}/`;
   do
-  echo 04_filter_samples/04_filtered/${projet}/${marker}/${run};
-  mkdir -p 05_assignment/01_runs/${projet}/${marker}/
-  cat 04_filter_samples/04_filtered/${projet}/${marker}/${run}/*.c.r.l.u.fasta > 05_assignment/01_runs/${projet}/${marker}/${run}.fasta
+  echo results/04_filter_samples/04_filtered/${projet}/${marker}/${run};
+  mkdir -p results/05_assignment/01_runs/${projet}/${marker}/
+  cat results/04_filter_samples/04_filtered/${projet}/${marker}/${run}/*.c.r.l.u.fasta > results/05_assignment/01_runs/${projet}/${marker}/${run}.fasta
   done
  done
 done
 ```
 
-sample files are concatenated by run
+sample files are concatenated by run into [results/05_assignment/01_runs](results/05_assignment/01_runs)
 
 ## 6 Assignment
 
 ```
 cd 05_assignment
-snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
+cd ..
 ```
 
-Assign each sequence to a taxon. Format the output into a csv results in folder [06_final_tables](06_final_tables)
\ No newline at end of file
+Assign each sequence to a taxon. Format the output into a csv results in folder [results/06_final_tables](results/06_final_tables)
\ No newline at end of file