ConcordanceCheck

Automation using Bash scripts and Cron jobs, inorder to automate the concordance check calculations.

Code style

Indentation:
environment variables: ALL_UPPERCASE_WITH_UNDERSCORES
global script variables: camelCase
local function variables: _camelCasePrefixedWithUnderscore
if ... then, while ... do and for ... do not on a single line, but on two lines with the then or do on the next line. E.g.
```
if ...
then
    ...
elif ...
then
    ...
fi
```

Version 1.x

See separate README_v1.md for details on the (deprecated) version

Version 2.x

Repo layout


|-- bin/......................... Bash scripts for managing data staging, data analysis and monitoring / error handling.
|-- etc/......................... Config files in bash syntax. Config files are sourced by the scripts in bin/.
|   |-- <group>.cfg.............. Group specific variables.
|   |-- <site>.cfg............... Site / server specific variables.
|   `-- sharedConfig.cfg......... Generic variables, which are the same for all group and all sites / servers.
`-- lib/
    `-- sharedFunctions.bash..... Generic functions for error handling, logging, track & trace, etc.

Data flow

      ⎛¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯⎞       ⎛¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯⎞
      ⎜ LFS  ⎜ The NGS_DNA pipeline is finished  ⎜>> + >>⎜ LFS  ⎜ The GAP pipeline is finished         ⎜ 
      ⎝__________________________________________⎠       ⎝_____________________________________________⎠
                                                    v
                                                    v  
                                                    v
   ⎛¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯⎞
   ⎜ LFS dat0*  ⎜ jobfile is put on dat06 in the /groups/umcg-gd/dat06/ConcordanceCheckSamplesheet folder                   ⎜ 
   ⎝__________________________________________________________________________________________________________________⎠
                                                    v
                                                    v <<<< 1: ParseDarwinSamplesheet.sh
                                                    v
   ⎛¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯⎞
   ⎜ LFS prm0*  ⎜ Script is executed by ateambot user, creating a samplesheet on TMP on the diagnostic cluster              ⎜
   ⎝__________________________________________________________________________________________________________________⎠
                                                    v
                                                    v <<<< 2: ConcordanceCheck.sh 
                                                    v
   ⎛¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯⎞
   ⎜ LFS  ⎜ Copies the ngs VCF and the array VCF file to tmp*.                                       ⎜
   ⎜ tmp* ⎜ Calculates concordance between the ngs and the array VCF files.                          ⎜
   ⎝_________________________________________________________________________________________________⎠
                                                    v
                                                    v
   ⎛¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯⎞
   ⎜ LFS  ⎜ Concordance check output is copied to prm0*.                                      ⎜ LFS   ⎜
   ⎜ tmp* ⎜ A file containing the location of the Concordance check output is stored on dat0* ⎜ prm0* ⎜
   ⎜      ⎜                                                                                   ⎜ dat0* ⎜
   ⎝_________________________________________________________________________________________________⎠
     v                                                                                           ^
     v                                                                                           ^
      `>>>>>>>>>>>>>>>> 3: CopyConcordanceData.sh >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>^

flow chaperone (prm06) --> leucine-zipper (tmp06) --> chaperone (prm06)

#### chaperone
###### umcg-gd-ateambot 
module load ConcordanceCheck/${version} ; ParseDarwinSamplesheet.sh -g umcg-gd -a umcg-gap

#### leucine-zipper
###### umcg-gd-ateambot 
module load ConcordanceCheck/${version} ; ConcordanceCheck.sh -g umcg-gd

#### chaperone
##### umcg-gd-dm
module load ConcordanceCheck/${version} ; CopyConcordanceData.sh -g umcg-gd

Job control flow

The path to phase.state files must be:

${TMP_ROOT_DIR}/logs/${ConcordanceCheckID}.${phase}.${state}

Phase is in most cases the name of the executing script as determined by ${SCRIPT_NAME}. State is either started, failed or finished.

## PROCESSING ##

ParseDarwinSamplesheet.sh -g NGSGROUP -a ARRAYGROUP => 


ConcordanceCheck.sh -g GROUP => ${cluster}:${TMP_ROOT_DIR}/logs/${project}/${run}.ConcordanceCheck.started
				${cluster}:${TMP_ROOT_DIR}/logs/${project}/${run}.ConcordanceCheck.finished

CopyConcordanceData.sh -g GROUP => ${cluster}:${PRM_ROOT_DIR}/concordance/logs/${ConcordanceCheckID}.CopyConcordanceCheckData.started
				${cluster}:${PRM_ROOT_DIR}/concordance/logs/${ConcordanceCheckID}.CopyConcordanceCheckData.finished

notifications.sh (Not (yet) for the concordancecheck, do we want this?)

To configure e-mail notification by the notifications script, edit the NOTIFY_FOR_PHASE_WITH_STATE array in etc/${group}.cfg and list the : combinations for which email should be sent. E.g.:

declare -a NOTIFY_FOR_PHASE_WITH_STATE=(
	'copyRawDataToPrm:failed'
	'copyRawDataToPrm:finished'
	'pipeline:failed'
	'copyProjectDataToPrm:failed'
	'copyProjectDataToPrm:finished'
)

In addition there must be a list of e-mail addresses (one address per line) for each state for which email notifications are enabled in:

${TMP_ROOT_DIR}/logs/${phase}.mailinglist

In case the list of addresses is the same for mutiple states, you can use symlinks per state. E.g.

${TMP_ROOT_DIR}/logs/all.mailinglist
${TMP_ROOT_DIR}/logs/${phase1}.mailinglist -> ./all.mailinglist${TMP_ROOT_DIR}/logs/${phase2}.mailinglist -> ./all.mailinglist

cleanup.sh (Not (yet) for the concordancecheck, do we want this?)

The cleanup script runs once a day, it will clean up old data:

Remove all the GavinStandAlone project/generatedscripts/tmp data once the GavinStandAlone has a ${project}.vcf.finished in ${TMP_ROOT_DIR}/GavinStandAlone/input
Clean up all the raw data that is older than 30 days, it first checks if the data is copied to prm
- check in the logs if ${filePrefix}.copyRawDataToPrm.sh.finished
- count *.fq.gz on tmp and prm and compare for an extra check
All the project + tmp data older than 30 days will also be deleted
- when ${project}.projectDataCopiedToPrm.sh.finished

Who runs what and where

Script	User	Running on site/server
1. ParseDarwinSamplesheet	${group}-ateambot	HPC Cluster with tmp mount
2. ConcordanceCheck	${group}-ateambot	HPC Cluster with tmp mount
3. copyConcordanceCheckData	${group}-dm	HPC Cluster with prm mount
4. notifications	${group}-ateambot	HPC Cluster with tmp mount
5. cleanup	${group}-ateambot	HPC Cluster with tmp mount

Location of job control and log files

LFS = logical file system; one of arc*, scr*, tmp* or prm*.
ConcordanceCheck has it's own dirs and does NOT touch/modify/create any data in the projects dir.

/groups/${group}/${LFS}/concordance
                 |-- samplesheets/
                 |   |-- ${ConcordanceCheckID}.sampleId.txt
                 |   |-- archive/
                 |-- logs/............................ Logs from ConcordanceCheck.
                 |       |-- ${ConcordanceCheckID}.${SCRIPT_NAME}.log
                 |       |-- ${ConcordanceCheckID}.${SCRIPT_NAME}.[started|failed|finished]
                 |       |-- ${ConcordanceCheckID}.${SCRIPT_NAME}.[started|failed|finished].mailed (not yet)
                 |-- jobs/
                 |-- array/
                 |   |-- ${arrayVcf}
                 |-- ngs/
                 |   |-- ${ngsVcf}
                 |-- results
                 |   |-- ${ConcordanceCheckID}.sample
                 |   |-- ${ConcordanceCheckID}.varinat
                 |-- heranalyse
                 |-- verificaties
                 |-- tmp

molgenis / ConcordanceCheck