[illumina_qc] Improve fastq channel building

Regex in Channel construction is too stringeant : '/**_R{1,2}(_*)?.fastq.gz'
By this way if fastq file name finish by R1.fastq.gz, it will be not add to the Channel.

changed milestone to %Next from 1.4.0

added Bug label

assigned to @jsabban

mentioned in commit 8a56d029

closed

reopened

The glob pattern is not reliable ! Need to be change !

Here are some rules of Nextflow glob pattern

• An asterisk, *, matches any number of characters (including none).
• Two asterisks, **, works like * but crosses directory boundaries. This syntax is generally used for matching complete paths.
• A question mark, ?, matches exactly one character.
• Braces specify a collection of subpatterns. For example:
  • {sun,moon,stars} matches "sun", "moon", or "stars".
  • {temp*,tmp*} matches all strings beginning with "temp" or "tmp".
• Square brackets convey a set of single characters or, when the hyphen character (-) is used, a range of characters. For example:
  • [aeiou] matches any lowercase vowel.
  • [0-9] matches any digit.
  • [A-Z] matches any uppercase letter.
  • [a-z,A-Z] matches any uppercase or lowercase letter.
    Within the square brackets, *, ?, and \ match themselves.
• All other characters match themselves.
• To match *, ?, or the other special characters, you can escape them by using the backslash character, . - For example: \ matches a single backslash, and ? matches the question mark.

Here are some examples of glob syntax

• *.html – Matches all strings that end in .html
• ??? – Matches all strings with exactly three letters or digits
• [0-9] – Matches all strings containing a numeric value
• *.{xml,bam,bai} – Matches any string ending with .xml, .bam or .bai
• a?*.fastq – Matches any string beginning with a, followed by at least one letter or digit, and ending with .fastq
• {foo*,[0-9]} – Matches any string beginning with foo or any string containing a numeric value

mentioned in commit e0ec2955

closed