jvarkit
NFHashTools
A tool to print and compare hashes .nextflow.log files
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar nfhashtools [options] Files
Usage: nfhashtools [options] Files
Options:
-g, --grep
Search for all those (sub)strings in 'hash' and 'value'. Case sensible .
The item matching all the regex are kept.
Default: []
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
-1
hide items unique to file1
Default: false
-2
hide items unique to file2
Default: false
-3
hide common items in file1 and file2
Default: false
-t
look only at 'value' matching that string
-u
hide common fields of the unique item in file1 and file2
Default: false
Keywords
- json
- nf
- nextflow
Creation Date
20251119
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite nfhashtools ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
Motivation
this tool looks for the log file of nextflow ( `.nextflow.log’) and generate a json output.
Requirement: Nextflow run must be launched with -dump-hashes json
If there is no file, the input is read on stdin.
If there is only one file, the hashes are collected, filtered and printed as JSON.
If there are two files. Both files are read and filtered. The JSON output contains
- a list of objects uniques to the file1,
- a list of objects uniques to the file2
- a list of common objects common to file1 and file2
If there only one object remaining in each list, an list of the common/discordant fields is also printed.
Example
$ sdiff newflow.1.log newflow.2.log
Nov-19 22:23:53.071 [Actor Thread 96] INFO nextflow.processo Nov-19 22:23:53.071 [Actor Thread 96] INFO nextflow.processo
{ {
"hash": "5350de1bf7fd1f286a1ad5baa7af30f5", | "hash": "ebc58ab2cb4848d04ec23d83f7ddf985",
"type": "java.util.UUID", "type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b" "value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
}, },
{ {
"hash": "f88ed0fa50638ac1efa458e70e21ebcc", "hash": "f88ed0fa50638ac1efa458e70e21ebcc",
"type": "java.lang.String", "type": "java.lang.String",
"value": "Hello" | "value": "Bonjour"
} }
] ]
Nov-19 22:23:53.071 [Actor Thread 96] INFO nextflow.processo Nov-19 22:23:53.071 [Actor Thread 96] INFO nextflow.processo
{ {
"hash": "1c72b78fd00c568c524095ff174b1a6f", "hash": "1c72b78fd00c568c524095ff174b1a6f",
"type": "java.util.UUID", "type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b" "value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
}, },
{ {
"hash": "cb2d18e15fc931db472229e671a76351", "hash": "cb2d18e15fc931db472229e671a76351",
"type": "java.lang.String", "type": "java.lang.String",
"value": "World" "value": "World"
} }
] ]
one file:
$ java -jar jvarkit.jar nfhashtools nextflow.1.log 2> /dev/null
[
[
{
"hash": "1c72b78fd00c568c524095ff174b1a6f",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
},
{
"hash": "cb2d18e15fc931db472229e671a76351",
"type": "java.lang.String",
"value": "World"
}
],
[
{
"hash": "5350de1bf7fd1f286a1ad5baa7af30f5",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
},
{
"hash": "f88ed0fa50638ac1efa458e70e21ebcc",
"type": "java.lang.String",
"value": "Hello"
}
]
]
one file with a filter:
$ java -jar jvarkit.jar nfhashtools -t Hello nextflow.1.log 2> /dev/null
[
[
{
"hash": "5350de1bf7fd1f286a1ad5baa7af30f5",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
},
{
"hash": "f88ed0fa50638ac1efa458e70e21ebcc",
"type": "java.lang.String",
"value": "Hello"
}
]
]
with two files
$ java -jar jvarkit.jar nfhashtools nextflow.1.log nextflow.2.log 2> /dev/null
[
{
"name": "L1",
"description": "Unique to nextflow.1.log",
"file": "nextflow.1.log",
"items": [
[
{
"hash": "5350de1bf7fd1f286a1ad5baa7af30f5",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
},
{
"hash": "f88ed0fa50638ac1efa458e70e21ebcc",
"type": "java.lang.String",
"value": "Hello"
}
]
]
},
{
"name": "L2",
"description": "Unique to nextflow.2.log",
"file": "nextflow.2.log",
"items": [
[
{
"hash": "ebc58ab2cb4848d04ec23d83f7ddf985",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
},
{
"hash": "f88ed0fa50638ac1efa458e70e21ebcc",
"type": "java.lang.String",
"value": "Bonjour"
}
]
]
},
{
"name": "L3",
"description": "common to nextflow.1.log and nextflow.2.log",
"file": [
"nextflow.1.log,
"nextflow.2.log"
],
"items": [
[
{
"hash": "1c72b78fd00c568c524095ff174b1a6f",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
},
{
"hash": "cb2d18e15fc931db472229e671a76351",
"type": "java.lang.String",
"value": "World"
}
]
]
},
{
"name": "uniq",
"description": "common/discordant values shared between the unique item of L1 and the unique item of L2",
"common": [],
"uniq_1": [
{
"hash": "f88ed0fa50638ac1efa458e70e21ebcc",
"type": "java.lang.String",
"value": "Hello"
},
{
"hash": "5350de1bf7fd1f286a1ad5baa7af30f5",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
}
],
"uniq_2": [
{
"hash": "f88ed0fa50638ac1efa458e70e21ebcc",
"type": "java.lang.String",
"value": "Bonjour"
},
{
"hash": "ebc58ab2cb4848d04ec23d83f7ddf985",
"type": "java.util.UUID",
"value": "7bae3014-6912-4d03-8e91-0db03ce8556b"
}
]
}
]