Merge branch 'master' of https://github.com/CCBR/CHARLIE

README.md

@@ -1,8 +1,22 @@
 # CHARLIE
 ![img](https://img.shields.io/github/issues/CCBR/CHARLIE?style=for-the-badge)![img](https://img.shields.io/github/forks/CCBR/CHARLIE?style=for-the-badge)![img](https://img.shields.io/github/stars/CCBR/CHARLIE?style=for-the-badge)![img](https://img.shields.io/github/license/CCBR/CHARLIE?style=for-the-badge)
 
- **C**ircrnas in **H**ost **A**nd vi**R**uses ana**L**ysis p**I**p**E**line
 
+### Table of Contents
+- [CHARLIE - **C**ircrnas in **H**ost **A**nd vi**R**uses ana**L**ysis p**I**p**E**line](#charlie)
+    - [Table of Contents](#table-of-contents)
+    - [1. Introduction](#1-introduction)
+    - [2. Flowchart](#2-flowchart)
+    - [3. Software Dependencies](#3-software-dependencies)
+    - [4. Usage](#4-usage)
+    - [5. License](#5-license)
+    - [6. Testing](#6-testing)
+      - [6.1 Test data](#61-test-data)
+      - [6.2 Expected output](#62-expected-output)
+
+### 1. Introduction
+
+ **C**ircrnas in **H**ost **A**nd vi**R**uses ana**L**ysis p**I**p**E**line
 
 Things to know about CHARLIE:
 
@@ -29,14 +43,46 @@ This circularRNA detection pipeline uses CIRCExplorer2, CIRI2 and many other too
 
 > Note: BWA<sup>1</sup>, BWA<sup>2</sup> denote 2 different alignment parameters, etc.
 
-Flowchart:
+### 2. Flowchart
 ![](docs/images/CHARLIE_v0.8.x.png)
 
-For complete documentation with tutorial go [here](https://ccbr.github.io/CCBR_circRNA_DAQ/).
+For complete documentation with tutorial go [here](https://CCBR.github.io/CHARLIE/).
 
 > DISCLAIMER: New circRNA tools have been added CHARLIE and the documentation is currently out of date!
 
-
+### 3. Software Dependencies
+
+The following version of various bioinformatics tools are using within CHARLIE:
+
+| tool          | version   |
+| ------------- | --------- |
+| blat          | 3.5       |
+| bedtools      | 2.30.0    |
+| bowtie        | 2-2.5.1   |
+| bowtie        | 1.3.1     |
+| bwa           | 0.7.17    |
+| circexplorer2 | 2.3.8     |
+| cufflinks     | 2.2.1     |
+| cutadapt      | 4.4       |
+| fastqc        | 0.11.9    |
+| hisat         | 2.2.2.1   |
+| java          | 18.0.1.1  |
+| multiqc       | 1.9       |
+| parallel      | 20231122  |
+| perl          | 5.34      |
+| picard        | 2.27.3    |
+| python        | 2.7       |
+| python        | 3.8       |
+| sambamba      | 0.8.2     |
+| samtools      | 1.16.1    |
+| STAR          | 2.7.6a    |
+| stringtie     | 2.2.1     |
+| ucsc          | 450       |
+| R             | 4.0.5     |
+| novocraft     | 4.03.05   |
+
+
+### 4. Usage
 
 ```bash
  % ./charlie
@@ -132,3 +178,134 @@ VersionInfo:
 
 ##########################################################################################
 ```
+
+### 5. License
+
+MIT License
+
+Copyright (c) 2021 Vishal Koparde
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+### 6. Testing
+
+#### Init
+
+Run init mode:
+
+```bash
+bash <path to charlie> -w=<path to output dir> -m=init
+```
+
+This will create the folder provided by `-w=`. The user should have write permission to this folder.
+
+#### Dry-run
+
+Test data (1 paired-end subsample and 1 single-end subsample) have been including under the `.tests/dummy_fastqs` folder. After running in `-m=init`, `samples.tsv` should be edited to point the copies of the above mentioned samples with the column headers:
+
+- sampleName	
+- path_to_R1_fastq	
+- path_to_R2_fastq
+
+Column `path_to_R2_fastq` will be blank in case of single-end samples.
+
+After editing `samples.tsv`, dry run should be run:
+
+```bash
+bash <path to charlie> -w=<path to output dir> -m=dryrun
+```
+
+This will create the reference fasta and gtf file based on the selections made in the `config.yaml`.
+
+#### Run
+If `-m=dryrun` was sucessful, then simply do `-m=run`. The output will look something like this
+
+```
+... ... skipping ~1000 lines
+...
+...
+Job stats:
+job                                              count    min threads    max threads
+---------------------------------------------  -------  ----------
+all                                                  1              1              1
+annotate_clear_output                                2              1              1
+circExplorer                                         2              2              2
+circExplorer_bwa                                     2              2              2
+circrnafinder                                        2              1              1
+ciri                                                 2             56             56
+clear                                                2              2              2
+create_bowtie2_index                                 1              1              1
+create_bwa_index                                     1              1              1
+create_circExplorer_BSJ_bam                          2              4              4
+create_circExplorer_linear_spliced_bams              2             56             56
+create_circExplorer_merged_found_counts_table        2              1              1
+create_hq_bams                                       2              1              1
+create_index                                         1             56             56
+create_master_counts_file                            1              1              1
+cutadapt                                             2             56             56
+dcc                                                  2              4              4
+dcc_create_samplesheets                              2              1              1
+estimate_duplication                                 2              1              1
+fastqc                                               2              4              4
+find_circ                                            2             56             56
+find_circ_align                                      2             56             56
+merge_SJ_tabs                                        1              2              2
+merge_alignment_stats                                1              1              1
+merge_genecounts                                     1              1              1
+merge_per_sample                                     2              1              1
+star1p                                               2             56             56
+star2p                                               2             56             56
+star_circrnafinder                                   2             56             56
+total                                               52              1             56
+
+Reasons:
+    (check individual jobs above for details)
+    input files updated by another job:
+        alignment_stats, all, annotate_clear_output, circExplorer, circExplorer_bwa, circrnafinder, ciri, clear, create_circExplorer_BSJ_bam, create_circExplorer_linear_spliced_bams, create_circExplorer_merged_found_counts_table, create_hq_bams, create_master_counts_file, dcc, dcc_create_samplesheets, estimate_duplication, fastqc, find_circ, find_circ_align, merge_SJ_tabs, merge_alignment_stats, merge_genecounts, merge_per_sample, star1p, star2p, star_circrnafinder
+    missing output files:
+        alignment_stats, annotate_clear_output, circExplorer, circExplorer_bwa, circrnafinder, ciri, clear, create_bowtie2_index, create_bwa_index, create_circExplorer_BSJ_bam, create_circExplorer_linear_spliced_bams, create_circExplorer_merged_found_counts_table, create_hq_bams, create_index, create_master_counts_file, cutadapt, dcc, dcc_create_samplesheets, estimate_duplication, fastqc, find_circ, find_circ_align, merge_SJ_tabs, merge_alignment_stats, merge_genecounts, merge_per_sample, star1p, star2p, star_circrnafinder
+
+This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
+Running...
+14743440
+```
+
+##### 6.1 Test Data
+
+The `.tests/dummy_fastqs` folder in the repo has test dataset:
+
+```bash
+% tree .tests/dummy_fastqs
+.tests/dummy_fastqs
+├── GI1_N.R1.fastq.gz
+├── GI1_N.R2.fastq.gz
+└── GI1_T.R1.fastq.gz
+```
+
+`GI1_N` is a PE sample while `GI1_T` is a SE sample.
+
+##### 6.2 Expected Output
+
+Expected output from the sample data is stored under `.tests/expected_output`.
+
+More details about running test data can be found [here](https://ccbr.github.io/CHARLIE/tutorial).
+
+> DISCLAIMER:
+> 
+> CHARLIE is built to be run only on [BIOWULF](https://hpc.nih.gov). A newer HPC-agnostic version of CHARLIE is planned for 2024.

charlie

@@ -7,6 +7,11 @@
 set -eo pipefail
 module purge
 
+# decide trigger
+trigger="mtime"
+# trigger="input"
+# trigger="code"
+
 ##########################################################################################
 # functions
 ##########################################################################################
@@ -36,10 +41,11 @@ GIT_COMMIT_TAG=$(get_git_commitid_tag $PIPELINE_HOME)
 ##########################################################################################
 
 CLUSTER_SBATCH_CMD="sbatch --parsable --cpus-per-task {cluster.threads} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --job-name {cluster.name} --output {cluster.output} --error {cluster.error}"
-if [ "$HOSTNAME" == "biowulf.nih.gov" ];then
+# if [ "$HOSTNAME" == "biowulf.nih.gov" ];then
+# if [ "$SLURM_CLUSTER_NAME" == "biowulf" ];then
   EXTRA_SINGULARITY_BINDS="/lscratch"
   CLUSTER_SBATCH_CMD="$CLUSTER_SBATCH_CMD --gres {cluster.gres}"
-fi
+# fi
 PYTHONVERSION="3.7"
 SNAKEMAKEVERSION="7.19.1"
 # SNAKEMAKEVERSION="5.24.1"
@@ -63,7 +69,7 @@ function usage() { cat << EOF
 
 ##########################################################################################
 
-Welcome to charlie(v0.9.0)
+Welcome to charlie(v0.10.0-dev)
  _______  __   __  _______  ______    ___      ___   _______ 
 |       ||  | |  ||   _   ||    _ |  |   |    |   | |       |
 |       ||  |_|  ||  |_|  ||   | ||  |   |    |   | |    ___|
@@ -293,6 +299,12 @@ function dryrun() {
   run "--dry-run" | tee ${WORKDIR}/dryrun.${timestamp}.log
 }
 
+function touch() {
+  runcheck
+  timestamp=$(date +"%y%m%d%H%M%S")
+  run "--touch" | tee ${WORKDIR}/touch.${timestamp}.log
+}
+
 ##########################################################################################
 # UNLOCK
 ##########################################################################################
@@ -367,7 +379,11 @@ function create_runinfo {
   echo "Pipeline Dir: $PIPELINE_HOME" > ${WORKDIR}/runinfo.yaml
   echo "Git Commit/Tag: $GIT_COMMIT_TAG" >> ${WORKDIR}/runinfo.yaml
   userlogin=$(whoami)
-  username=$(finger $userlogin|grep ^Login|awk -F"Name: " '{print $2}')
+  if [[ `which finger 2>/dev/null` ]];then 
+	  username=$(finger $userlogin |grep ^Login | awk -F"Name: " '{print $2}'); 
+  elif [[ `which lslogins 2>/dev/null` ]];then 
+	  username=$(lslogins -u $userlogin | grep ^Geco | awk -F": " '{print $2}' | awk '{$1=$1;print}'); 
+  else username="";fi
   echo "Login: $userlogin" >> ${WORKDIR}/runinfo.yaml
   echo "Name: $username" >> ${WORKDIR}/runinfo.yaml
   g=$(groups)
@@ -435,7 +451,7 @@ function run() {
   --configfile $CONFIGFILE \
   --cores all \
   --rerun-incomplete \
-  --rerun-triggers input \
+  --rerun-triggers $trigger \
   --retries 2 \
   --keep-going \
   --stats ${WORKDIR}/snakemake.stats \
@@ -457,7 +473,7 @@ function run() {
 #SBATCH --job-name="charlie"
 #SBATCH --mem=40g
 #SBATCH --partition="ccr,norm"
-#SBATCH --time=96:00:00
+#SBATCH --time=48:00:00
 #SBATCH --cpus-per-task=2
 
 module load python/$PYTHONVERSION
@@ -479,7 +495,7 @@ snakemake -s $SNAKEFILE \
 --cluster-status $CLUSTERSTATUSCMD \
 -j 500 \
 --rerun-incomplete \
---rerun-triggers input \
+--rerun-triggers $trigger \
 --retries 2 \
 --keep-going \
 --stats ${WORKDIR}/snakemake.stats \
@@ -496,8 +512,17 @@ EOF
 
   sbatch ${WORKDIR}/submit_script.sbatch
 
+  elif [ "$1" == "--touch" ];then
+
+snakemake $1 -s $SNAKEFILE \
+--directory $WORKDIR \
+--configfile $CONFIGFILE \
+--cores 1
+
   else # dry-run and unlock
 
+echo $CLUSTER_SBATCH_CMD
+
 snakemake $1 -s $SNAKEFILE \
 --directory $WORKDIR \
 --use-envmodules \
@@ -508,7 +533,7 @@ snakemake $1 -s $SNAKEFILE \
 --cluster "$CLUSTER_SBATCH_CMD" \
 -j 500 \
 --rerun-incomplete \
---rerun-triggers input \
+--rerun-triggers $trigger \
 --keep-going \
 --reason \
 --stats ${WORKDIR}/snakemake.stats
@@ -597,6 +622,7 @@ function main(){
     run) runslurm && exit 0;;
     runlocal) runlocal && exit 0;;
     reset) reset && exit 0;;
+    touch) touch && exit 0;;
     dry) dryrun && exit 0;;                      # hidden option
     local) runlocal && exit 0;;                  # hidden option
     reconfig) reconfig && exit 0;;               # hidden option for debugging

config/config.yaml

@@ -27,8 +27,9 @@ run_nclscan: False
 nclscan_config: "WORKDIR/nclscan.config"
 #
 # Should we also run find_circ? True or False WITHOUT quotes
-run_findcirc: True
-
+run_findcirc: False
+# findcirc_params: "--noncanonical --allhits" # this gives way too many circRNAs
+findcirc_params: "--noncanonical"
 
 
 # select references .... host + viruses(comma-separated):
@@ -90,15 +91,17 @@ tools: "PIPELINE_HOME/resources/tools.yaml"
 cluster: "WORKDIR/cluster.json"
 
 adapters: "PIPELINE_HOME/resources/TruSeq_and_nextera_adapters.consolidated.fa"
-circexplorer_bsj_circRNA_min_reads: 2 # in addition to "known" and "low-conf" circRNAs identified by circexplorer, we also include those found in back_spliced.bed file but not classified as known/low-conf only if the number of reads supporting the BSJ call is greater than this number
-minreadcount: 2 # this is used to filter circRNAs while creating the per-sample counts table
+circexplorer_bsj_circRNA_min_reads: 3 # in addition to "known" and "low-conf" circRNAs identified by circexplorer, we also include those found in back_spliced.bed file but not classified as known/low-conf only if the number of reads supporting the BSJ call is greater than this number
+minreadcount: 3 # this is used to filter circRNAs while creating the per-sample counts table
 flanksize: 18 # 18bp flank on either side of the BSJ .. used by multiple BSJ callers
 dcc_strandedness: "-ss" # "-ss" for stranded library and "--nonstrand" for unstranded
 cutadapt_min_length: 15
 cutadapt_n: 5
 cutadapt_max_n: 0.5
 cutadapt_O: 5
 cutadapt_q: 20
+high_confidence_core_callers: "circExplorer,circExplorer_bwa"
+high_confidence_core_callers_plus_n: 1
 
 ciri_perl_script: "/data/CCBR_Pipeliner/bin/CIRI_v2.0.6/CIRI2.pl"
 nclscan_dir: "/data/CCBR_Pipeliner/bin/NCLscan-1.7.0"

config/samples.tsv

@@ -1,3 +1,3 @@
 sampleName	path_to_R1_fastq	path_to_R2_fastq
-GI1_N	/data/CCBR_Pipeliner/test_datasets/circRNA/human/GI1_N_ss.R1.fastq.gz	/data/CCBR_Pipeliner/test_datasets/circRNA/human/GI1_N_ss.R2.fastq.gz
-GI1_T	/data/CCBR_Pipeliner/test_datasets/circRNA/human/GI1_T_ss.R1.fastq.gz
+GI1_N	/data/CCBR_Pipeliner/testdata/circRNA/human/GI1_N_ss.R1.fastq.gz	/data/CCBR_Pipeliner/testdata/circRNA/human/GI1_N_ss.R2.fastq.gz
+GI1_T	/data/CCBR_Pipeliner/testdata/circRNA/human/GI1_T_ss.R1.fastq.gz

docs/flowchart.md

@@ -1,8 +1,9 @@
-# circRNA DAQ Pipeline
+# CHARLIE
 
 ![img](https://img.shields.io/github/issues/kopardev/circRNA?style=for-the-badge)![img](https://img.shields.io/github/forks/kopardev/circRNA?style=for-the-badge)![img](https://img.shields.io/github/stars/kopardev/circRNA?style=for-the-badge)![img](https://img.shields.io/github/license/kopardev/circRNA?style=for-the-badge)
 
-Flowchart for [v0.3.3](https://github.com/kopardev/circRNA/releases/tag/v0.3.3):
+Flowchart
 
-![img](circRNA_v0.3.3.png)
+![img](images/CHARLIE_v0.8.x.png)
 
+> DISCLAIMER: This chart is for v0.8.x may be slightly outdated.