Wigan Athletic boss on Tranmere shoot-out win, Stephen Humphrys redemption and Charlie Wyke return
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The Prenton Park encounter ended 0-0, with the home side recording the only effort on target during the 90 minutes.
Latics dominated in almost every area only to fail to really work the home goalkeeper, before winning 6-5 on spot-kicks.
"The end result was great for sure," said Maloney. "In terms of the performance, I actually liked a lot of what I saw.
"Even when they tried to press us, I thought we tried to play through them.
"In my opinion, maybe with the penalties at the end, I thought we deserved to win the game on the whole.
"We certainly had enough chances to win it, but I was really happy with the players.
"Some of these players haven't played a lot of minutes recently.
"I honestly thought we set the tone after 30 seconds, when Charlie Wyke really put a sprint in and won the ball from one of their players.
"I was happy with a lot of what we did."
Maloney had been forced to make 10 changes to his line-up - due to international call-ups and injuries - with only Omar Rekik keeping his place.
"You're always worried with the players who haven't played too much," acknowledged the Latics boss.
"But I thought the actual performance - and I know the game ended 0-0 - I was very happy with.
"We train very hard...I give every player the same information, I don't concentrate on the 'starting XI'...it's always about the squad.
"I really am aware of the squad, and I think that showed.
"The movement that they had, the understanding of each other's position, was good.
"And the last four weeks as a whole have been very positive."
The Scot referenced Stephen Humphrys, who thumped home his penalty, three days after missing from 12 yards in Saturday's 1-1 league draw at Cheltenham.
"The penalties were very good, and I was really pleased for Humps as well," he said.
"I really wanted Stephen to take a penalty, and he really stepped up."
Maloney also highlighted the performance of striker Wyke, who was handed the captain's armband after a frustrating few weeks watching in from the outside.
The 30-year-old missed a couple of decent chances in either half, before being withdrawn midway through the second half.
"Charlie's fine," confirmed Maloney.
"The plan was always for him to play 60 minutes, he hasn't played too much recently.
"But I was really happy with Charlie.
"I think he could have scored a couple, but I was really happy with the mentality he's been showing.
"We've got a number of '9s' pushing for positions, but Charlie is a brilliant finisher, and a really big member of our squad.
"I chose him as one of our captains, and he really led by example.
"I was happy with his performance, he'll rest up and he'll be ready to go again."
It was a relatively uneventful encounter, with Tranmere having the one and only effort on target in the 90 minutes.
Callum McManaman, Humphrys, Tom Pearce and Chris Sze scored in the shoot-out before Josh Stones and James Balagizi missed.
Harry McHugh and Kell Watts nudged Latics ahead, before Ben Amos pulled off a super save to ensure Latics topped their group.