Merge pull request #325 from sateeshperi/dev

fix ignore params help text [ci skip]

nextflow_schema.json

@@ -305,28 +305,28 @@
                     "type": "integer",
                     "default": 0,
                     "description": "Ignore methylation in first n bases of 5' end of R1",
-                    "help_text": "Ignore the first 0 bp from the 5' end of Read 1 (or single-end alignment files) when processing the methylation call string. This can remove e.g. a restriction enzyme site at the start of each read or any other source of bias (such as PBAT-Seq data).",
+                    "help_text": "Ignore the first <int> bp from the 5' end of Read 1 (or single-end alignment files) when processing the methylation call string. This can remove e.g. a restriction enzyme site at the start of each read or any other source of bias (such as PBAT-Seq data).",
                     "fa_icon": "far fa-eye-slash"
                 },
                 "ignore_r2": {
                     "type": "integer",
                     "default": 2,
                     "description": "Ignore methylation in first n bases of 5' end of R2",
-                    "help_text": "Ignore the first 2 bp from the 5' end of Read 2 of paired-end sequencing results only. Since the first couple of bases in Read 2 of BS-Seq experiments show a severe bias towards non-methylation as a result of end-repairing sonicated fragments with unmethylated cytosines (see M-bias plot), it is recommended that the first couple of bp of Read 2 are removed before starting downstream analysis. Please see the section on M-bias plots in the Bismark User Guide for more details.",
+                    "help_text": "Ignore the first <int> bp from the 5' end of Read 2 of paired-end sequencing results only. Since the first couple of bases in Read 2 of BS-Seq experiments show a severe bias towards non-methylation as a result of end-repairing sonicated fragments with unmethylated cytosines (see M-bias plot), it is recommended that the first couple of bp of Read 2 are removed before starting downstream analysis. Please see the section on M-bias plots in the Bismark User Guide for more details.",
                     "fa_icon": "far fa-eye-slash"
                 },
                 "ignore_3prime_r1": {
                     "type": "integer",
                     "default": 0,
                     "description": "Ignore methylation in last n bases of 3' end of R1",
-                    "help_text": "Ignore the first 0 bp from the 5' end of Read 2 of paired-end sequencing results only. Since the first couple of bases in Read 2 of BS-Seq experiments show a severe bias towards non-methylation as a result of end-repairing sonicated fragments with unmethylated cytosines (see M-bias plot), it is recommended that the first couple of bp of Read 2 are removed before starting downstream analysis. Please see the section on M-bias plots in the Bismark User Guide for more details.",
+                    "help_text": "Ignore the first <int> bp from the 5' end of Read 2 of paired-end sequencing results only. Since the first couple of bases in Read 2 of BS-Seq experiments show a severe bias towards non-methylation as a result of end-repairing sonicated fragments with unmethylated cytosines (see M-bias plot), it is recommended that the first couple of bp of Read 2 are removed before starting downstream analysis. Please see the section on M-bias plots in the Bismark User Guide for more details.",
                     "fa_icon": "far fa-eye-slash"
                 },
                 "ignore_3prime_r2": {
                     "type": "integer",
                     "default": 2,
                     "description": "Ignore methylation in last n bases of 3' end of R2",
-                    "help_text": "Ignore the last 2 bp from the 3' end of Read 1 (or single-end alignment files) when processing the methylation call string. This can remove unwanted biases from the end of reads.",
+                    "help_text": "Ignore the last <int> bp from the 3' end of Read 1 (or single-end alignment files) when processing the methylation call string. This can remove unwanted biases from the end of reads.",
                     "fa_icon": "far fa-eye-slash"
                 },
                 "known_splices": {